diff --git a/tests/integration/test_cli.py b/tests/integration/test_cli.py
new file mode 100644
index 0000000..55fbb27
--- /dev/null
+++ b/tests/integration/test_cli.py
@@ -0,0 +1,209 @@
+"""Integration tests for CLI commands."""
+
+import pytest
+import tempfile
+import os
+from pathlib import Path
+from typer.testing import CliRunner
+from docgen.cli import app
+
+
+class TestCLIDetect:
+    """Tests for detect command."""
+
+    def test_detect_no_files(self):
+        """Test detect with empty directory."""
+        runner = CliRunner()
+        
+        with tempfile.TemporaryDirectory() as tmpdir:
+            result = runner.invoke(app, ["detect", tmpdir])
+            assert result.exit_code == 0
+            assert "No endpoints found" in result.output
+
+    def test_detect_python_fastapi(self):
+        """Test detect with FastAPI code."""
+        runner = CliRunner()
+        
+        code = '''
+from fastapi import FastAPI
+app = FastAPI()
+
+@app.get("/users")
+def get_users():
+    return {"users": []}
+
+@app.post("/users")
+def create_user():
+    return {"id": 1}
+'''
+        with tempfile.TemporaryDirectory() as tmpdir:
+            py_file = Path(tmpdir) / "main.py"
+            py_file.write_text(code)
+            
+            result = runner.invoke(app, ["detect", tmpdir])
+            assert result.exit_code == 0
+            assert "Found" in result.output or "endpoints" in result.output.lower()
+
+    def test_detect_with_framework_filter(self):
+        """Test detect with specific framework."""
+        runner = CliRunner()
+        
+        code = '''
+from flask import Flask
+app = Flask(__name__)
+
+@app.route("/items")
+def get_items():
+    return {"items": []}
+'''
+        with tempfile.TemporaryDirectory() as tmpdir:
+            py_file = Path(tmpdir) / "app.py"
+            py_file.write_text(code)
+            
+            result = runner.invoke(app, ["detect", tmpdir, "--framework", "python"])
+            assert result.exit_code == 0
+
+
+class TestCLIGenerate:
+    """Tests for generate command."""
+
+    def test_generate_html(self):
+        """Test HTML generation."""
+        runner = CliRunner()
+        
+        code = '''
+from fastapi import FastAPI
+app = FastAPI()
+
+@app.get("/users")
+def get_users():
+    return {"users": []}
+'''
+        with tempfile.TemporaryDirectory() as tmpdir:
+            py_file = Path(tmpdir) / "main.py"
+            py_file.write_text(code)
+            
+            output_dir = Path(tmpdir) / "docs"
+            result = runner.invoke(app, [
+                "generate",
+                tmpdir,
+                "--output", str(output_dir),
+                "--format", "html",
+            ])
+            
+            assert result.exit_code == 0
+            assert output_dir.exists()
+            assert (output_dir / "index.html").exists()
+
+    def test_generate_markdown(self):
+        """Test Markdown generation."""
+        runner = CliRunner()
+        
+        code = '''
+from fastapi import FastAPI
+app = FastAPI()
+
+@app.get("/items")
+def get_items():
+    return {"items": []}
+'''
+        with tempfile.TemporaryDirectory() as tmpdir:
+            py_file = Path(tmpdir) / "main.py"
+            py_file.write_text(code)
+            
+            output_dir = Path(tmpdir) / "docs"
+            result = runner.invoke(app, [
+                "generate",
+                tmpdir,
+                "--output", str(output_dir),
+                "--format", "markdown",
+            ])
+            
+            assert result.exit_code == 0
+            assert (output_dir / "README.md").exists()
+
+    def test_generate_openapi(self):
+        """Test OpenAPI generation."""
+        runner = CliRunner()
+        
+        code = '''
+from fastapi import FastAPI
+app = FastAPI()
+
+@app.get("/products")
+def get_products():
+    return {"products": []}
+'''
+        with tempfile.TemporaryDirectory() as tmpdir:
+            py_file = Path(tmpdir) / "main.py"
+            py_file.write_text(code)
+            
+            output_dir = Path(tmpdir) / "api"
+            result = runner.invoke(app, [
+                "generate",
+                tmpdir,
+                "--output", str(output_dir),
+                "--format", "openapi",
+            ])
+            
+            assert result.exit_code == 0
+            assert (output_dir / "openapi.json").exists()
+
+    def test_generate_with_custom_title(self):
+        """Test generation with custom title."""
+        runner = CliRunner()
+        
+        code = '''
+from fastapi import FastAPI
+app = FastAPI()
+
+@app.get("/test")
+def get_test():
+    return {}
+'''
+        with tempfile.TemporaryDirectory() as tmpdir:
+            py_file = Path(tmpdir) / "main.py"
+            py_file.write_text(code)
+            
+            output_dir = Path(tmpdir) / "docs"
+            result = runner.invoke(app, [
+                "generate",
+                tmpdir,
+                "--output", str(output_dir),
+                "--title", "My Custom API",
+                "--description", "A custom API description",
+                "--version", "2.0.0",
+            ])
+            
+            assert result.exit_code == 0
+            content = (output_dir / "index.html").read_text()
+            assert "My Custom API" in content
+            assert "A custom API description" in content
+            assert "2.0.0" in content
+
+
+class TestCLIInit:
+    """Tests for init command."""
+
+    def test_init_creates_config(self):
+        """Test init command creates configuration file."""
+        runner = CliRunner()
+        
+        with tempfile.TemporaryDirectory() as tmpdir:
+            result = runner.invoke(app, ["init", "--output", tmpdir])
+            
+            assert result.exit_code == 0
+            config_file = Path(tmpdir) / "docgen.toml"
+            assert config_file.exists()
+
+
+class TestCLIVersion:
+    """Tests for version command."""
+
+    def test_version_shows_version(self):
+        """Test version command displays version."""
+        runner = CliRunner()
+        result = runner.invoke(app, ["version"])
+        
+        assert result.exit_code == 0
+        assert "DocGen-CLI" in result.output