diff --git a/packages/core/schematics/migrations/undecorated-classes-with-di/index.ts b/packages/core/schematics/migrations/undecorated-classes-with-di/index.ts
index 7ffce12ee6039..801910df1ca2f 100644
--- a/packages/core/schematics/migrations/undecorated-classes-with-di/index.ts
+++ b/packages/core/schematics/migrations/undecorated-classes-with-di/index.ts
@@ -9,6 +9,7 @@
 import {logging} from '@angular-devkit/core';
 import {Rule, SchematicContext, SchematicsException, Tree} from '@angular-devkit/schematics';
 import {AotCompiler} from '@angular/compiler';
+import {Diagnostic as NgDiagnostic} from '@angular/compiler-cli';
 import {PartialEvaluator} from '@angular/compiler-cli/src/ngtsc/partial_evaluator';
 import {TypeScriptReflectionHost} from '@angular/compiler-cli/src/ngtsc/reflection';
 import {relative} from 'path';
@@ -84,10 +85,11 @@ function runUndecoratedClassesMigration(
   const partialEvaluator =
       new PartialEvaluator(new TypeScriptReflectionHost(typeChecker), typeChecker);
   const declarationCollector = new NgDeclarationCollector(typeChecker, partialEvaluator);
-  const rootSourceFiles = program.getRootFileNames().map(f => program.getSourceFile(f) !);
+  const sourceFiles = program.getSourceFiles().filter(
+      s => !s.isDeclarationFile && !program.isSourceFileFromExternalLibrary(s));
 
   // Analyze source files by detecting all directives, components and providers.
-  rootSourceFiles.forEach(sourceFile => declarationCollector.visitNode(sourceFile));
+  sourceFiles.forEach(sourceFile => declarationCollector.visitNode(sourceFile));
 
   const {decoratedDirectives, decoratedProviders, undecoratedDeclarations} = declarationCollector;
   const transform =
@@ -151,14 +153,28 @@ function runUndecoratedClassesMigration(
   }
 }
 
+function getErrorDiagnostics(diagnostics: ReadonlyArray<ts.Diagnostic|NgDiagnostic>) {
+  return <ts.Diagnostic[]>diagnostics.filter(d => d.category === ts.DiagnosticCategory.Error);
+}
+
 function gracefullyCreateProgram(
     tree: Tree, basePath: string, tsconfigPath: string,
     logger: logging.LoggerApi): {compiler: AotCompiler, program: ts.Program}|null {
   try {
     const {ngcProgram, host, program, compiler} = createNgcProgram(
         (options) => createMigrationCompilerHost(tree, options, basePath), tsconfigPath);
-    const syntacticDiagnostics = ngcProgram.getTsSyntacticDiagnostics();
-    const structuralDiagnostics = ngcProgram.getNgStructuralDiagnostics();
+    const syntacticDiagnostics = getErrorDiagnostics(ngcProgram.getTsSyntacticDiagnostics());
+    const structuralDiagnostics = getErrorDiagnostics(ngcProgram.getNgStructuralDiagnostics());
+    const configDiagnostics = getErrorDiagnostics(
+        [...program.getOptionsDiagnostics(), ...ngcProgram.getNgOptionDiagnostics()]);
+
+    if (configDiagnostics.length) {
+      logger.warn(
+          `\nTypeScript project "${tsconfigPath}" has configuration errors. This could cause ` +
+          `an incomplete migration. Please fix the following failures and rerun the migration:`);
+      logger.error(ts.formatDiagnostics(configDiagnostics, host));
+      return null;
+    }
 
     // Syntactic TypeScript errors can throw off the query analysis and therefore we want
     // to notify the developer that we couldn't analyze parts of the project. Developers
diff --git a/packages/core/schematics/test/undecorated_classes_with_di_migration_spec.ts b/packages/core/schematics/test/undecorated_classes_with_di_migration_spec.ts
index 15ea12c7f2b8e..beebaf81b4ff8 100644
--- a/packages/core/schematics/test/undecorated_classes_with_di_migration_spec.ts
+++ b/packages/core/schematics/test/undecorated_classes_with_di_migration_spec.ts
@@ -1495,5 +1495,32 @@ describe('Undecorated classes with DI migration', () => {
       expect(warnOutput.length).toBe(0);
       expect(errorOutput.length).toBe(0);
     });
+
+    it('should not throw if tsconfig references non-existent source file', async() => {
+      writeFile('/tsconfig.json', JSON.stringify({
+        compilerOptions: {
+          lib: ['es2015'],
+        },
+        files: [
+          './non-existent.ts',
+        ]
+      }));
+
+      let failed = false;
+      try {
+        await runMigration();
+      } catch (e) {
+        failed = true;
+      }
+
+      expect(failed).toBe(false, 'Expected the migration not to fail.');
+      expect(warnOutput.length).toBe(1);
+      expect(errorOutput.length).toBe(1);
+      expect(warnOutput[0])
+          .toContain(
+              'TypeScript project "tsconfig.json" has configuration errors. This could cause an ' +
+              'incomplete migration. Please fix the following failures and rerun the migration:');
+      expect(errorOutput[0]).toMatch(/non-existent\.ts' not found/);
+    });
   });
 });