diff --git a/src/compiler/program.ts b/src/compiler/program.ts
index a1861f6b462..d86a80a5387 100644
--- a/src/compiler/program.ts
+++ b/src/compiler/program.ts
@@ -358,7 +358,8 @@ namespace ts {
     export function createProgram(rootNames: string[], options: CompilerOptions, host?: CompilerHost, oldProgram?: Program): Program {
         let program: Program;
         let files: SourceFile[] = [];
-        let diagnostics = createDiagnosticCollection();
+        let fileProcessingDiagnostics = createDiagnosticCollection();
+        let programDiagnostics = createDiagnosticCollection();
 
         let commonSourceDirectory: string;
         let diagnosticsProducingTypeChecker: TypeChecker;
@@ -428,6 +429,7 @@ namespace ts {
             getIdentifierCount: () => getDiagnosticsProducingTypeChecker().getIdentifierCount(),
             getSymbolCount: () => getDiagnosticsProducingTypeChecker().getSymbolCount(),
             getTypeCount: () => getDiagnosticsProducingTypeChecker().getTypeCount(),
+            getFileProcessingDiagnostics: () => fileProcessingDiagnostics
         };
         return program;
 
@@ -460,6 +462,7 @@ namespace ts {
             
             // check if program source files has changed in the way that can affect structure of the program
             let newSourceFiles: SourceFile[] = [];
+            let modifiedSourceFiles: SourceFile[] = [];
             for (let oldSourceFile of oldProgram.getSourceFiles()) {
                 let newSourceFile = host.getSourceFile(oldSourceFile.fileName, options.target);
                 if (!newSourceFile) {
@@ -499,6 +502,7 @@ namespace ts {
                     }
                     // pass the cache of module resolutions from the old source file
                     newSourceFile.resolvedModules = oldSourceFile.resolvedModules;
+                    modifiedSourceFiles.push(newSourceFile);
                 }
                 else {
                     // file has no changes - use it as is
@@ -515,7 +519,11 @@ namespace ts {
             }
             
             files = newSourceFiles;
+            fileProcessingDiagnostics = oldProgram.getFileProcessingDiagnostics();
             
+            for (let modifiedFile of modifiedSourceFiles) {
+                fileProcessingDiagnostics.reattachFileDiagnostics(modifiedFile);
+            }
             oldProgram.structureIsReused = true;
                 
             return true;
@@ -645,9 +653,10 @@ namespace ts {
                 Debug.assert(!!sourceFile.bindDiagnostics);
                 let bindDiagnostics = sourceFile.bindDiagnostics;
                 let checkDiagnostics = typeChecker.getDiagnostics(sourceFile, cancellationToken);
-                let programDiagnostics = diagnostics.getDiagnostics(sourceFile.fileName);
+                let fileProcessingDiagnosticsInFile = fileProcessingDiagnostics.getDiagnostics(sourceFile.fileName);
+                let programDiagnosticsInFile = programDiagnostics.getDiagnostics(sourceFile.fileName);
 
-                return bindDiagnostics.concat(checkDiagnostics).concat(programDiagnostics);
+                return bindDiagnostics.concat(checkDiagnostics).concat(fileProcessingDiagnosticsInFile).concat(programDiagnosticsInFile);
             });
         }
 
@@ -664,7 +673,8 @@ namespace ts {
 
         function getOptionsDiagnostics(): Diagnostic[] {
             let allDiagnostics: Diagnostic[] = [];
-            addRange(allDiagnostics, diagnostics.getGlobalDiagnostics());
+            addRange(allDiagnostics, fileProcessingDiagnostics.getGlobalDiagnostics())
+            addRange(allDiagnostics, programDiagnostics.getGlobalDiagnostics());
             return sortAndDeduplicateDiagnostics(allDiagnostics);
         }
 
@@ -772,10 +782,10 @@ namespace ts {
 
             if (diagnostic) {
                 if (refFile !== undefined && refEnd !== undefined && refPos !== undefined) {
-                    diagnostics.add(createFileDiagnostic(refFile, refPos, refEnd - refPos, diagnostic, ...diagnosticArgument));
+                    fileProcessingDiagnostics.add(createFileDiagnostic(refFile, refPos, refEnd - refPos, diagnostic, ...diagnosticArgument));
                 }
                 else {
-                    diagnostics.add(createCompilerDiagnostic(diagnostic, ...diagnosticArgument));
+                    fileProcessingDiagnostics.add(createCompilerDiagnostic(diagnostic, ...diagnosticArgument));
                 }
             }
         }
@@ -797,11 +807,11 @@ namespace ts {
                 // We haven't looked for this file, do so now and cache result
                 let file = host.getSourceFile(fileName, options.target, hostErrorMessage => {
                     if (refFile !== undefined && refPos !== undefined && refEnd !== undefined) {
-                        diagnostics.add(createFileDiagnostic(refFile, refPos, refEnd - refPos,
+                        fileProcessingDiagnostics.add(createFileDiagnostic(refFile, refPos, refEnd - refPos,
                             Diagnostics.Cannot_read_file_0_Colon_1, fileName, hostErrorMessage));
                     }
                     else {
-                        diagnostics.add(createCompilerDiagnostic(Diagnostics.Cannot_read_file_0_Colon_1, fileName, hostErrorMessage));
+                        fileProcessingDiagnostics.add(createCompilerDiagnostic(Diagnostics.Cannot_read_file_0_Colon_1, fileName, hostErrorMessage));
                     }
                 });
                 filesByName.set(canonicalName, file);
@@ -837,11 +847,11 @@ namespace ts {
                     let sourceFileName = useAbsolutePath ? getNormalizedAbsolutePath(file.fileName, host.getCurrentDirectory()) : file.fileName;
                     if (canonicalName !== sourceFileName) {
                         if (refFile !== undefined && refPos !== undefined && refEnd !== undefined) {
-                            diagnostics.add(createFileDiagnostic(refFile, refPos, refEnd - refPos,
+                            fileProcessingDiagnostics.add(createFileDiagnostic(refFile, refPos, refEnd - refPos,
                                 Diagnostics.File_name_0_differs_from_already_included_file_name_1_only_in_casing, fileName, sourceFileName));
                         }
                         else {
-                            diagnostics.add(createCompilerDiagnostic(Diagnostics.File_name_0_differs_from_already_included_file_name_1_only_in_casing, fileName, sourceFileName));
+                            fileProcessingDiagnostics.add(createCompilerDiagnostic(Diagnostics.File_name_0_differs_from_already_included_file_name_1_only_in_casing, fileName, sourceFileName));
                         }
                     }
                 }
@@ -877,7 +887,7 @@ namespace ts {
             return;
 
             function findModuleSourceFile(fileName: string, nameLiteral: Expression) {
-                return findSourceFile(fileName, /* isDefaultLib */ false, file, nameLiteral.pos, nameLiteral.end);
+                return findSourceFile(fileName, /* isDefaultLib */ false, file, skipTrivia(file.text, nameLiteral.pos), nameLiteral.end);
             }
         }
 
@@ -902,7 +912,7 @@ namespace ts {
                 for (let i = 0, n = Math.min(commonPathComponents.length, sourcePathComponents.length); i < n; i++) {
                     if (commonPathComponents[i] !== sourcePathComponents[i]) {
                         if (i === 0) {
-                            diagnostics.add(createCompilerDiagnostic(Diagnostics.Cannot_find_the_common_subdirectory_path_for_the_input_files));
+                            programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Cannot_find_the_common_subdirectory_path_for_the_input_files));
                             return;
                         }
 
@@ -931,7 +941,7 @@ namespace ts {
                     if (!isDeclarationFile(sourceFile)) {
                         let absoluteSourceFilePath = host.getCanonicalFileName(getNormalizedAbsolutePath(sourceFile.fileName, currentDirectory));
                         if (absoluteSourceFilePath.indexOf(absoluteRootDirectoryPath) !== 0) {
-                            diagnostics.add(createCompilerDiagnostic(Diagnostics.File_0_is_not_under_rootDir_1_rootDir_is_expected_to_contain_all_source_files, sourceFile.fileName, options.rootDir));
+                            programDiagnostics.add(createCompilerDiagnostic(Diagnostics.File_0_is_not_under_rootDir_1_rootDir_is_expected_to_contain_all_source_files, sourceFile.fileName, options.rootDir));
                             allFilesBelongToPath = false;
                         }
                     }
@@ -944,52 +954,52 @@ namespace ts {
         function verifyCompilerOptions() {
             if (options.isolatedModules) {
                 if (options.declaration) {
-                    diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "declaration", "isolatedModules"));
+                    programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "declaration", "isolatedModules"));
                 }
 
                 if (options.noEmitOnError) {
-                    diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "noEmitOnError", "isolatedModules"));
+                    programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "noEmitOnError", "isolatedModules"));
                 }
 
                 if (options.out) {
-                    diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "out", "isolatedModules"));
+                    programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "out", "isolatedModules"));
                 }
 
                 if (options.outFile) {
-                    diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "outFile", "isolatedModules"));
+                    programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "outFile", "isolatedModules"));
                 }
             }
 
             if (options.inlineSourceMap) {
                 if (options.sourceMap) {
-                    diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "sourceMap", "inlineSourceMap"));
+                    programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "sourceMap", "inlineSourceMap"));
                 }
                 if (options.mapRoot) {
-                    diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "mapRoot", "inlineSourceMap"));
+                    programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "mapRoot", "inlineSourceMap"));
                 }
                 if (options.sourceRoot) {
-                    diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "sourceRoot", "inlineSourceMap"));
+                    programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "sourceRoot", "inlineSourceMap"));
                 }
             }
 
 
             if (options.inlineSources) {
                 if (!options.sourceMap && !options.inlineSourceMap) {
-                    diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_inlineSources_can_only_be_used_when_either_option_inlineSourceMap_or_option_sourceMap_is_provided));
+                    programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_inlineSources_can_only_be_used_when_either_option_inlineSourceMap_or_option_sourceMap_is_provided));
                 }
             }
 
             if (options.out && options.outFile) {
-                diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "out", "outFile"));
+                programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "out", "outFile"));
             }
 
             if (!options.sourceMap && (options.mapRoot || options.sourceRoot)) {
                 // Error to specify --mapRoot or --sourceRoot without mapSourceFiles
                 if (options.mapRoot) {
-                    diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_without_specifying_option_1, "mapRoot", "sourceMap"));
+                    programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_without_specifying_option_1, "mapRoot", "sourceMap"));
                 }
                 if (options.sourceRoot) {
-                    diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_without_specifying_option_1, "sourceRoot", "sourceMap"));
+                    programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_without_specifying_option_1, "sourceRoot", "sourceMap"));
                 }
                 return;
             }
@@ -1000,24 +1010,24 @@ namespace ts {
             let firstExternalModuleSourceFile = forEach(files, f => isExternalModule(f) ? f : undefined);
             if (options.isolatedModules) {
                 if (!options.module && languageVersion < ScriptTarget.ES6) {
-                    diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_isolatedModules_can_only_be_used_when_either_option_module_is_provided_or_option_target_is_ES6_or_higher));
+                    programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_isolatedModules_can_only_be_used_when_either_option_module_is_provided_or_option_target_is_ES6_or_higher));
                 }
 
                 let firstNonExternalModuleSourceFile = forEach(files, f => !isExternalModule(f) && !isDeclarationFile(f) ? f : undefined);
                 if (firstNonExternalModuleSourceFile) {
                     let span = getErrorSpanForNode(firstNonExternalModuleSourceFile, firstNonExternalModuleSourceFile);
-                    diagnostics.add(createFileDiagnostic(firstNonExternalModuleSourceFile, span.start, span.length, Diagnostics.Cannot_compile_namespaces_when_the_isolatedModules_flag_is_provided));
+                    programDiagnostics.add(createFileDiagnostic(firstNonExternalModuleSourceFile, span.start, span.length, Diagnostics.Cannot_compile_namespaces_when_the_isolatedModules_flag_is_provided));
                 }
             }
             else if (firstExternalModuleSourceFile && languageVersion < ScriptTarget.ES6 && !options.module) {
                 // We cannot use createDiagnosticFromNode because nodes do not have parents yet
                 let span = getErrorSpanForNode(firstExternalModuleSourceFile, firstExternalModuleSourceFile.externalModuleIndicator);
-                diagnostics.add(createFileDiagnostic(firstExternalModuleSourceFile, span.start, span.length, Diagnostics.Cannot_compile_modules_unless_the_module_flag_is_provided));
+                programDiagnostics.add(createFileDiagnostic(firstExternalModuleSourceFile, span.start, span.length, Diagnostics.Cannot_compile_modules_unless_the_module_flag_is_provided));
             }
 
             // Cannot specify module gen target when in es6 or above
             if (options.module && languageVersion >= ScriptTarget.ES6) {
-                diagnostics.add(createCompilerDiagnostic(Diagnostics.Cannot_compile_modules_into_commonjs_amd_system_or_umd_when_targeting_ES6_or_higher));
+                programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Cannot_compile_modules_into_commonjs_amd_system_or_umd_when_targeting_ES6_or_higher));
             }
 
             // there has to be common source directory if user specified --outdir || --sourceRoot
@@ -1046,30 +1056,30 @@ namespace ts {
 
             if (options.noEmit) {
                 if (options.out) {
-                    diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "noEmit", "out"));
+                    programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "noEmit", "out"));
                 }
 
                 if (options.outFile) {
-                    diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "noEmit", "outFile"));
+                    programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "noEmit", "outFile"));
                 }
 
                 if (options.outDir) {
-                    diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "noEmit", "outDir"));
+                    programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "noEmit", "outDir"));
                 }
 
                 if (options.declaration) {
-                    diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "noEmit", "declaration"));
+                    programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "noEmit", "declaration"));
                 }
             }
 
             if (options.emitDecoratorMetadata &&
                 !options.experimentalDecorators) {
-                diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_without_specifying_option_1, "emitDecoratorMetadata", "experimentalDecorators"));
+                programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_without_specifying_option_1, "emitDecoratorMetadata", "experimentalDecorators"));
             }
 
             if (options.experimentalAsyncFunctions &&
                 options.target !== ScriptTarget.ES6) {
-                diagnostics.add(createCompilerDiagnostic(Diagnostics.Option_experimentalAsyncFunctions_cannot_be_specified_when_targeting_ES5_or_lower));
+                programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_experimentalAsyncFunctions_cannot_be_specified_when_targeting_ES5_or_lower));
             }
         }
     }
diff --git a/src/compiler/types.ts b/src/compiler/types.ts
index 47182e39527..265fa5c86fb 100644
--- a/src/compiler/types.ts
+++ b/src/compiler/types.ts
@@ -1359,6 +1359,7 @@ namespace ts {
         /* @internal */ getSymbolCount(): number;
         /* @internal */ getTypeCount(): number;
 
+        /* @internal */ getFileProcessingDiagnostics(): DiagnosticCollection;
         // For testing purposes only.
         /* @internal */ structureIsReused?: boolean;
     }
@@ -2322,5 +2323,7 @@ namespace ts {
         // operation caused diagnostics to be returned by storing and comparing the return value
         // of this method before/after the operation is performed.
         getModificationCount(): number;
+        
+        /* @internal */ reattachFileDiagnostics(newFile: SourceFile): void;
     }
 }
diff --git a/src/compiler/utilities.ts b/src/compiler/utilities.ts
index 99ea06532a0..6c5bd8df95d 100644
--- a/src/compiler/utilities.ts
+++ b/src/compiler/utilities.ts
@@ -1507,12 +1507,23 @@ namespace ts {
             add,
             getGlobalDiagnostics,
             getDiagnostics,
-            getModificationCount
+            getModificationCount,
+            reattachFileDiagnostics
         };
 
         function getModificationCount() {
             return modificationCount;
         }
+        
+        function reattachFileDiagnostics(newFile: SourceFile): void {
+            if (!hasProperty(fileDiagnostics, newFile.fileName)) {
+                return;
+            }
+            
+            for (let diagnostic of fileDiagnostics[newFile.fileName]) {
+                diagnostic.file = newFile;
+            }
+        }
 
         function add(diagnostic: Diagnostic): void {
             let diagnostics: Diagnostic[];
diff --git a/tests/cases/unittests/reuseProgramStructure.ts b/tests/cases/unittests/reuseProgramStructure.ts
index 6c043299c8f..56b1dedbcbb 100644
--- a/tests/cases/unittests/reuseProgramStructure.ts
+++ b/tests/cases/unittests/reuseProgramStructure.ts
@@ -184,7 +184,11 @@ module ts {
     describe("Reuse program structure", () => {
         let target = ScriptTarget.Latest;
         let files = [
-            { name: "a.ts", text: SourceText.New(`/// <reference path='b.ts'/>`, "", `var x = 1`) },
+            { name: "a.ts", text: SourceText.New(
+                `
+/// <reference path='b.ts'/>
+/// <reference path='non-existing-file.ts'/>
+`, "",`var x = 1`) },
             { name: "b.ts", text: SourceText.New(`/// <reference path='c.ts'/>`, "", `var y = 2`) },
             { name: "c.ts", text: SourceText.New("", "", `var z = 1;`) },
         ]
@@ -195,6 +199,9 @@ module ts {
                 files[0].text = files[0].text.updateProgram("var x = 100");
             });
             assert.isTrue(program_1.structureIsReused);
+            let program1Diagnostics = program_1.getSemanticDiagnostics(program_1.getSourceFile("a.ts"))
+            let program2Diagnostics = program_2.getSemanticDiagnostics(program_1.getSourceFile("a.ts"))
+            assert.equal(program1Diagnostics.length, program2Diagnostics.length);
         });
 
         it("fails if change affects tripleslash references", () => {