diff --git a/src/compiler/commandLineParser.ts b/src/compiler/commandLineParser.ts
index e15cd5df7db..f386c701dd7 100644
--- a/src/compiler/commandLineParser.ts
+++ b/src/compiler/commandLineParser.ts
@@ -1341,12 +1341,21 @@ namespace ts {
             return Array(paddingLength + 1).join(" ");
         }
 
+        function isAllowedOption({ category, name }: CommandLineOption): boolean {
+            // Skip options which do not have a category or have category `Command_line_Options`
+            // Exclude all possible `Advanced_Options` in tsconfig.json which were NOT defined in command line
+            return category !== undefined
+                && category !== Diagnostics.Command_line_Options
+                && (category !== Diagnostics.Advanced_Options || compilerOptionsMap.has(name));
+        }
+
         function writeConfigurations() {
             // Filter applicable options to place in the file
             const categorizedOptions = createMultiMap<CommandLineOption>();
             for (const option of optionDeclarations) {
                 const { category } = option;
-                if (category !== undefined && category !== Diagnostics.Command_line_Options && category !== Diagnostics.Advanced_Options) {
+
+                if (isAllowedOption(option)) {
                     categorizedOptions.add(getLocaleSpecificMessage(category), option);
                 }
             }
diff --git a/src/harness/unittests/initializeTSConfig.ts b/src/harness/unittests/initializeTSConfig.ts
index f1f57808e55..b67fce6226f 100644
--- a/src/harness/unittests/initializeTSConfig.ts
+++ b/src/harness/unittests/initializeTSConfig.ts
@@ -30,5 +30,7 @@ namespace ts {
         initTSConfigCorrectly("Initialized TSConfig with incorrect compiler option", ["--init", "--someNonExistOption"]);
 
         initTSConfigCorrectly("Initialized TSConfig with incorrect compiler option value", ["--init", "--lib", "nonExistLib,es5,es2015.promise"]);
+
+        initTSConfigCorrectly("Initialized TSConfig with advanced options", ["--init", "--declaration", "--declarationDir", "lib", "--skipLibCheck", "--noErrorTruncation"]);
     });
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/tsConfig/Initialized TSConfig with advanced options/tsconfig.json b/tests/baselines/reference/tsConfig/Initialized TSConfig with advanced options/tsconfig.json
new file mode 100644
index 00000000000..c75fe3c9dc6
--- /dev/null
+++ b/tests/baselines/reference/tsConfig/Initialized TSConfig with advanced options/tsconfig.json	
@@ -0,0 +1,63 @@
+{
+  "compilerOptions": {
+    /* Basic Options */
+    "target": "es5",                          /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017','ES2018' or 'ESNEXT'. */
+    "module": "commonjs",                     /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', or 'ESNext'. */
+    // "lib": [],                             /* Specify library files to be included in the compilation. */
+    // "allowJs": true,                       /* Allow javascript files to be compiled. */
+    // "checkJs": true,                       /* Report errors in .js files. */
+    // "jsx": "preserve",                     /* Specify JSX code generation: 'preserve', 'react-native', or 'react'. */
+    "declaration": true,                      /* Generates corresponding '.d.ts' file. */
+    // "declarationMap": true,                /* Generates a sourcemap for each corresponding '.d.ts' file. */
+    // "sourceMap": true,                     /* Generates corresponding '.map' file. */
+    // "outFile": "./",                       /* Concatenate and emit output to single file. */
+    // "outDir": "./",                        /* Redirect output structure to the directory. */
+    // "rootDir": "./",                       /* Specify the root directory of input files. Use to control the output directory structure with --outDir. */
+    // "removeComments": true,                /* Do not emit comments to output. */
+    // "noEmit": true,                        /* Do not emit outputs. */
+    // "importHelpers": true,                 /* Import emit helpers from 'tslib'. */
+    // "downlevelIteration": true,            /* Provide full support for iterables in 'for-of', spread, and destructuring when targeting 'ES5' or 'ES3'. */
+    // "isolatedModules": true,               /* Transpile each file as a separate module (similar to 'ts.transpileModule'). */
+
+    /* Strict Type-Checking Options */
+    "strict": true,                           /* Enable all strict type-checking options. */
+    // "noImplicitAny": true,                 /* Raise error on expressions and declarations with an implied 'any' type. */
+    // "strictNullChecks": true,              /* Enable strict null checks. */
+    // "strictFunctionTypes": true,           /* Enable strict checking of function types. */
+    // "strictPropertyInitialization": true,  /* Enable strict checking of property initialization in classes. */
+    // "noImplicitThis": true,                /* Raise error on 'this' expressions with an implied 'any' type. */
+    // "alwaysStrict": true,                  /* Parse in strict mode and emit "use strict" for each source file. */
+
+    /* Additional Checks */
+    // "noUnusedLocals": true,                /* Report errors on unused locals. */
+    // "noUnusedParameters": true,            /* Report errors on unused parameters. */
+    // "noImplicitReturns": true,             /* Report error when not all code paths in function return a value. */
+    // "noFallthroughCasesInSwitch": true,    /* Report errors for fallthrough cases in switch statement. */
+
+    /* Module Resolution Options */
+    // "moduleResolution": "node",            /* Specify module resolution strategy: 'node' (Node.js) or 'classic' (TypeScript pre-1.6). */
+    // "baseUrl": "./",                       /* Base directory to resolve non-absolute module names. */
+    // "paths": {},                           /* A series of entries which re-map imports to lookup locations relative to the 'baseUrl'. */
+    // "rootDirs": [],                        /* List of root folders whose combined content represents the structure of the project at runtime. */
+    // "typeRoots": [],                       /* List of folders to include type definitions from. */
+    // "types": [],                           /* Type declaration files to be included in compilation. */
+    // "allowSyntheticDefaultImports": true,  /* Allow default imports from modules with no default export. This does not affect code emit, just typechecking. */
+    "esModuleInterop": true,                  /* Enables emit interoperability between CommonJS and ES Modules via creation of namespace objects for all imports. Implies 'allowSyntheticDefaultImports'. */
+    // "preserveSymlinks": true,              /* Do not resolve the real path of symlinks. */
+
+    /* Source Map Options */
+    // "sourceRoot": "./",                    /* Specify the location where debugger should locate TypeScript files instead of source locations. */
+    // "mapRoot": "./",                       /* Specify the location where debugger should locate map files instead of generated locations. */
+    // "inlineSourceMap": true,               /* Emit a single file with source maps instead of having a separate file. */
+    // "inlineSources": true,                 /* Emit the source alongside the sourcemaps within a single file; requires '--inlineSourceMap' or '--sourceMap' to be set. */
+
+    /* Experimental Options */
+    // "experimentalDecorators": true,        /* Enables experimental support for ES7 decorators. */
+    // "emitDecoratorMetadata": true,         /* Enables experimental support for emitting type metadata for decorators. */
+
+    /* Advanced Options */
+    "noErrorTruncation": true,                /* Do not truncate error messages. */
+    "declarationDir": "lib",                  /* Output directory for generated declaration files. */
+    "skipLibCheck": true                      /* Skip type checking of declaration files. */
+  }
+}
\ No newline at end of file