diff --git a/cmd/zoekt-indexserver/config.go b/cmd/zoekt-indexserver/config.go
index 0a73bef..d976904 100644
--- a/cmd/zoekt-indexserver/config.go
+++ b/cmd/zoekt-indexserver/config.go
@@ -195,7 +195,7 @@
 			cmd.Args = append(cmd.Args, c.CGitURL)
 		} else if c.BitBucketServerURL != "" {
 			cmd = exec.Command("zoekt-mirror-bitbucket-server",
-				"-dest", repoDir, "-url", c.BitBucketServerURL)
+				"-dest", repoDir, "-url", c.BitBucketServerURL, "-delete")
 			if c.BitBucketServerProject != "" {
 				cmd.Args = append(cmd.Args, "-project", c.BitBucketServerProject)
 			}
diff --git a/cmd/zoekt-mirror-bitbucket-server/main.go b/cmd/zoekt-mirror-bitbucket-server/main.go
index 790d075..19270ec 100644
--- a/cmd/zoekt-mirror-bitbucket-server/main.go
+++ b/cmd/zoekt-mirror-bitbucket-server/main.go
@@ -1,5 +1,3 @@
-// Copyright 2016 Google Inc. All rights reserved.
-//
 // Licensed under the Apache License, Version 2.0 (the "License");
 // you may not use this file except in compliance with the License.
 // You may obtain a copy of the License at
@@ -41,6 +39,7 @@
 	serverUrl := flag.String("url", "", "BitBucket Server url")
 	credentialsFile := flag.String("credentials", ".bitbucket-credentials", "file holding BitBucket Server credentials")
 	project := flag.String("project", "", "project to mirror")
+	deleteRepos := flag.Bool("delete", false, "delete missing repos")
 	namePattern := flag.String("name", "", "only clone repos whose name matches the given regexp.")
 	excludePattern := flag.String("exclude", "", "don't mirror repos whose names match this regexp.")
 	projectType := flag.String("type", "", "only clone repos whose type matches the given string. "+
@@ -137,6 +136,36 @@
 	if err := cloneRepos(destDir, rootURL.Host, repos, password); err != nil {
 		log.Fatalf("cloneRepos: %v", err)
 	}
+
+	if *deleteRepos {
+		if err := deleteStaleRepos(*dest, filter, repos); err != nil {
+			log.Fatalf("deleteStaleRepos: %v", err)
+		}
+	}
+}
+
+func deleteStaleRepos(destDir string, filter *gitindex.Filter, repos []bitbucketv1.Repository) error {
+	var baseURL string
+	if len(repos) > 0 {
+		baseURL = repos[0].Links.Self[0].Href
+	} else {
+		return nil
+	}
+	u, err := url.Parse(baseURL)
+	if err != nil {
+		return err
+	}
+	u.Path = ""
+
+	names := map[string]struct{}{}
+	for _, r := range repos {
+		names[filepath.Join(u.Host, r.Project.Key, r.Slug+".git")] = struct{}{}
+	}
+
+	if err := gitindex.DeleteRepos(destDir, u, names, filter); err != nil {
+		log.Fatalf("deleteRepos: %v", err)
+	}
+	return nil
 }
 
 func IsValidProjectType(projectType string) bool {
diff --git a/cmd/zoekt-mirror-github/main.go b/cmd/zoekt-mirror-github/main.go
index c1848ca..7a2078b 100644
--- a/cmd/zoekt-mirror-github/main.go
+++ b/cmd/zoekt-mirror-github/main.go
@@ -170,39 +170,17 @@
 	}
 	u.Path = user
 
-	paths, err := gitindex.ListRepos(destDir, u)
-	if err != nil {
-		return err
-	}
-
-	names := map[string]bool{}
+	names := map[string]struct{}{}
 	for _, r := range repos {
 		u, err := url.Parse(*r.HTMLURL)
 		if err != nil {
 			return err
 		}
 
-		names[filepath.Join(u.Host, u.Path+".git")] = true
+		names[filepath.Join(u.Host, u.Path+".git")] = struct{}{}
 	}
-	var toDelete []string
-	for _, p := range paths {
-		if filter.Include(filepath.Base(p)) && !names[p] {
-			toDelete = append(toDelete, p)
-		}
-	}
-
-	if len(toDelete) > 0 {
-		log.Printf("deleting repos %v", toDelete)
-	}
-
-	var errs []string
-	for _, d := range toDelete {
-		if err := os.RemoveAll(filepath.Join(destDir, d)); err != nil {
-			errs = append(errs, err.Error())
-		}
-	}
-	if len(errs) > 0 {
-		return fmt.Errorf("errors: %v", errs)
+	if err := gitindex.DeleteRepos(destDir, u, names, filter); err != nil {
+		log.Fatalf("deleteRepos: %v", err)
 	}
 	return nil
 }
diff --git a/cmd/zoekt-mirror-gitlab/main.go b/cmd/zoekt-mirror-gitlab/main.go
index 8e156de..7f1fa40 100644
--- a/cmd/zoekt-mirror-gitlab/main.go
+++ b/cmd/zoekt-mirror-gitlab/main.go
@@ -146,40 +146,18 @@
 		return err
 	}
 
-	paths, err := gitindex.ListRepos(destDir, u)
-	if err != nil {
-		return err
-	}
-
-	names := map[string]bool{}
+	names := map[string]struct{}{}
 	for _, p := range projects {
 		u, err := url.Parse(p.HTTPURLToRepo)
 		if err != nil {
 			return err
 		}
 
-		names[filepath.Join(u.Host, u.Path)] = true
+		names[filepath.Join(u.Host, u.Path)] = struct{}{}
 	}
 
-	var toDelete []string
-	for _, p := range paths {
-		if filter.Include(p) && !names[p] {
-			toDelete = append(toDelete, p)
-		}
-	}
-
-	if len(toDelete) > 0 {
-		log.Printf("deleting repos %v", toDelete)
-	}
-
-	var errs []string
-	for _, d := range toDelete {
-		if err := os.RemoveAll(filepath.Join(destDir, d)); err != nil {
-			errs = append(errs, err.Error())
-		}
-	}
-	if len(errs) > 0 {
-		return fmt.Errorf("errors: %v", errs)
+	if err := gitindex.DeleteRepos(destDir, u, names, filter); err != nil {
+		log.Fatalf("deleteRepos: %v", err)
 	}
 	return nil
 }
diff --git a/gitindex/delete.go b/gitindex/delete.go
new file mode 100644
index 0000000..f53e1af
--- /dev/null
+++ b/gitindex/delete.go
@@ -0,0 +1,41 @@
+package gitindex
+
+import (
+	"fmt"
+	"log"
+	"net/url"
+	"os"
+	"path/filepath"
+)
+
+// DeleteRepos deletes stale repos under a specific path in disk. The `names`
+// argument stores names of repos retrieved from the git hosting site
+// and is used along with the `filter` argument to decide on repo deletion.
+func DeleteRepos(baseDir string, urlPrefix *url.URL, names map[string]struct{}, filter *Filter) error {
+	paths, err := ListRepos(baseDir, urlPrefix)
+	if err != nil {
+		return err
+	}
+	var toDelete []string
+	for _, p := range paths {
+		_, exists := names[p]
+		if filter.Include(filepath.Base(p)) && !exists {
+			toDelete = append(toDelete, p)
+		}
+	}
+
+	if len(toDelete) > 0 {
+		log.Printf("deleting repos %v", toDelete)
+	}
+
+	var errs []string
+	for _, d := range toDelete {
+		if err := os.RemoveAll(filepath.Join(baseDir, d)); err != nil {
+			errs = append(errs, err.Error())
+		}
+	}
+	if len(errs) > 0 {
+		return fmt.Errorf("errors: %v", errs)
+	}
+	return nil
+}
diff --git a/gitindex/delete_test.go b/gitindex/delete_test.go
new file mode 100644
index 0000000..571a25d
--- /dev/null
+++ b/gitindex/delete_test.go
@@ -0,0 +1,83 @@
+package gitindex
+
+import (
+	"io/ioutil"
+	"net/url"
+	"path/filepath"
+	"reflect"
+	"testing"
+)
+
+func TestDeleteRepos(t *testing.T) {
+	dir, err := ioutil.TempDir("", "")
+	if err != nil {
+		t.Fatalf("TempDir: %v", err)
+	}
+
+	if err := createSubmoduleRepo(dir); err != nil {
+		t.Error("createSubmoduleRepo", err)
+	}
+
+	reposBefore, err := FindGitRepos(dir)
+	if err != nil {
+		t.Error("FindGitRepos", err)
+	}
+
+	gotBefore := map[string]struct{}{}
+	for _, r := range reposBefore {
+		p, err := filepath.Rel(dir, r)
+		if err != nil {
+			t.Fatalf("Relative: %v", err)
+		}
+
+		gotBefore[p] = struct{}{}
+	}
+
+	wantBefore := map[string]struct{}{
+		"gerrit.googlesource.com/bdir.git":     {},
+		"gerrit.googlesource.com/sub/bdir.git": {},
+		"adir/.git":                            {},
+		"bdir/.git":                            {},
+		"gerrit.googlesource.com/adir.git":     {},
+	}
+
+	if !reflect.DeepEqual(gotBefore, wantBefore) {
+		t.Fatalf("got %v want %v", gotBefore, wantBefore)
+	}
+
+	aURL, _ := url.Parse("http://gerrit.googlesource.com")
+	aURL.Path = "sub"
+	names := map[string]struct{}{
+		"bdir/.git":                        {},
+		"gerrit.googlesource.com/adir.git": {},
+	}
+	filter, _ := NewFilter("", "")
+
+	err = DeleteRepos(dir, aURL, names, filter)
+	if err != nil {
+		t.Fatalf("DeleteRepos: %T", err)
+	}
+	reposAfter, err := FindGitRepos(dir)
+	if err != nil {
+		t.Error("FindGitRepos", err)
+	}
+
+	gotAfter := map[string]struct{}{}
+	for _, r := range reposAfter {
+		p, err := filepath.Rel(dir, r)
+		if err != nil {
+			t.Fatalf("Relative: %v", err)
+		}
+
+		gotAfter[p] = struct{}{}
+	}
+	wantAfter := map[string]struct{}{
+		"gerrit.googlesource.com/bdir.git": {},
+		"adir/.git":                        {},
+		"bdir/.git":                        {},
+		"gerrit.googlesource.com/adir.git": {}}
+
+	if !reflect.DeepEqual(gotAfter, wantAfter) {
+		t.Errorf("got %v want %v", gotAfter, wantAfter)
+	}
+}