diff --git a/src/haiku/rag/app.py b/src/haiku/rag/app.py
index 51e63751..d5926312 100644
--- a/src/haiku/rag/app.py
+++ b/src/haiku/rag/app.py
@@ -192,9 +192,9 @@ class HaikuRAGApp:
                     f"[yellow]Document with id {doc_id} not found.[/yellow]"
                 )
 
-    async def search(self, query: str, limit: int = 5):
+    async def search(self, query: str, limit: int = 5, filter: str | None = None):
         async with HaikuRAG(db_path=self.db_path) as self.client:
-            results = await self.client.search(query, limit=limit)
+            results = await self.client.search(query, limit=limit, filter=filter)
             if not results:
                 self.console.print("[yellow]No results found.[/yellow]")
                 return
diff --git a/src/haiku/rag/cli.py b/src/haiku/rag/cli.py
index 1d778487..1cc04154 100644
--- a/src/haiku/rag/cli.py
+++ b/src/haiku/rag/cli.py
@@ -221,6 +221,12 @@ def search(
         "-l",
         help="Maximum number of results to return",
     ),
+    filter: str | None = typer.Option(
+        None,
+        "--filter",
+        "-f",
+        help="SQL WHERE clause to filter documents (e.g., \"uri LIKE '%arxiv%'\")",
+    ),
     db: Path = typer.Option(
         Config.storage.data_dir / "haiku.rag.lancedb",
         "--db",
@@ -230,7 +236,7 @@ def search(
     from haiku.rag.app import HaikuRAGApp
 
     app = HaikuRAGApp(db_path=db)
-    asyncio.run(app.search(query=query, limit=limit))
+    asyncio.run(app.search(query=query, limit=limit, filter=filter))
 
 
 @cli.command("ask", help="Ask a question using the QA agent")