diff --git a/src/lib/converter/converter.ts b/src/lib/converter/converter.ts
index c22680ce6..f011da057 100644
--- a/src/lib/converter/converter.ts
+++ b/src/lib/converter/converter.ts
@@ -10,6 +10,7 @@ import { ConverterComponent, ConverterNodeComponent, ConverterTypeComponent, Typ
 import { CompilerHost } from './utils/compiler-host';
 import { Component, Option, ChildableComponent, ComponentClass } from '../utils/component';
 import { normalizePath } from '../utils/fs';
+import { createMinimatch } from '../utils/paths';
 
 /**
  * Result structure of the [[Converter.convert]] method.
@@ -384,26 +385,33 @@ export class Converter extends ChildableComponent<Application, ConverterComponen
     private compile(context: Context): ReadonlyArray<ts.Diagnostic> {
         const program = context.program;
 
-        program.getSourceFiles().forEach((sourceFile) => {
+        const exclude = createMinimatch(this.application.exclude || []);
+        const isExcluded = (file: ts.SourceFile) => exclude.some(mm => mm.match(file.fileName));
+
+        const includedSourceFiles = program.getSourceFiles()
+            .filter(file => !isExcluded(file));
+        const isRelevantError = ({ file }: ts.Diagnostic) => !file || includedSourceFiles.includes(file);
+
+        includedSourceFiles.forEach((sourceFile) => {
             this.convertNode(context, sourceFile);
         });
 
-        let diagnostics = program.getOptionsDiagnostics();
+        let diagnostics = program.getOptionsDiagnostics().filter(isRelevantError);
         if (diagnostics.length) {
             return diagnostics;
         }
 
-        diagnostics = program.getSyntacticDiagnostics();
+        diagnostics = program.getSyntacticDiagnostics().filter(isRelevantError);
         if (diagnostics.length) {
             return diagnostics;
         }
 
-        diagnostics = program.getGlobalDiagnostics();
+        diagnostics = program.getGlobalDiagnostics().filter(isRelevantError);
         if (diagnostics.length) {
             return diagnostics;
         }
 
-        diagnostics = program.getSemanticDiagnostics();
+        diagnostics = program.getSemanticDiagnostics().filter(isRelevantError);
         if (diagnostics.length) {
             return diagnostics;
         }
diff --git a/src/test/module/a.ts b/src/test/module/a.ts
new file mode 100644
index 000000000..129b9c31a
--- /dev/null
+++ b/src/test/module/a.ts
@@ -0,0 +1,5 @@
+import { multiply } from './b';
+
+export function add(a: number, b: number) {
+    return a + multiply(b, 1);
+}
diff --git a/src/test/module/b.ts b/src/test/module/b.ts
new file mode 100644
index 000000000..f0fc5ed2d
--- /dev/null
+++ b/src/test/module/b.ts
@@ -0,0 +1,3 @@
+export function multiply(a: number, b: number) {
+    return a * b;
+}
diff --git a/src/test/typedoc.ts b/src/test/typedoc.ts
index 977bf858a..f223c4c1b 100644
--- a/src/test/typedoc.ts
+++ b/src/test/typedoc.ts
@@ -2,12 +2,13 @@ import { Application } from '..';
 import * as Path from 'path';
 import Assert = require('assert');
 import './.dot';
+import { Converter, Context } from '../lib/converter';
 
 describe('TypeDoc', function() {
     let application: Application;
 
     describe('Application', function() {
-        it('constructs', function() {
+        before('constructs', function() {
             application = new Application();
         });
         it('expands input directory', function() {
@@ -64,5 +65,17 @@ describe('TypeDoc', function() {
             Assert.equal(expanded.indexOf(Path.join(inputFiles, '.dot', 'index.d.ts')), -1);
             Assert.equal(expanded.indexOf(inputFiles), -1);
         });
+        it('Honors the exclude option even if a module is imported', () => {
+            application.options.setValue('exclude', '**/b.d.ts');
+
+            function handler(context: Context) {
+                Assert.deepStrictEqual(context.fileNames, [
+                    Path.resolve(__dirname, 'module', 'a.d.ts').replace(/\\/g, '/')
+                ]);
+            }
+            application.converter.on(Converter.EVENT_END, handler);
+            application.convert([ Path.join(__dirname, 'module', 'a.d.ts')]);
+            application.converter.off(Converter.EVENT_END, handler);
+        });
     });
 });
diff --git a/tsconfig.json b/tsconfig.json
index 2195896e8..ded73fcfa 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -6,7 +6,8 @@
       "es5",
       "es2015.core",
       "es2015.collection",
-      "es2015.iterable"
+      "es2015.iterable",
+      "es2016.array.include" // Supported by Node 6+
     ],
     "target": "es2015",
     "noImplicitAny": false,