diff --git a/cmd/ipfs/init.go b/cmd/ipfs/init.go
index 2861901fb..ebc5f6069 100644
--- a/cmd/ipfs/init.go
+++ b/cmd/ipfs/init.go
@@ -51,6 +51,7 @@ at ~/.ipfs. To change the repo location, set the $IPFS_PATH environment variable
 
 		log.Info("checking if daemon is running...")
 		if daemonLocked {
+			log.Debug("Ipfs daemon is running.")
 			e := "ipfs daemon is running. please stop it to run this command"
 			return cmds.ClientError(e)
 		}
diff --git a/cmd/ipfs/ipfs.go b/cmd/ipfs/ipfs.go
index 179d6cfb7..57b6e9091 100644
--- a/cmd/ipfs/ipfs.go
+++ b/cmd/ipfs/ipfs.go
@@ -105,4 +105,5 @@ var cmdDetailsMap = map[*cmds.Command]cmdDetails{
 	commands.CommandsDaemonCmd: {doesNotUseRepo: true},
 	commands.VersionCmd:        {doesNotUseConfigAsInput: true, doesNotUseRepo: true}, // must be permitted to run before init
 	commands.LogCmd:            {cannotRunOnClient: true},
+	commands.RepoFsckCmd:       {cannotRunOnDaemon: true},
 }
diff --git a/cmd/ipfs/main.go b/cmd/ipfs/main.go
index 563c83e10..40757f9df 100644
--- a/cmd/ipfs/main.go
+++ b/cmd/ipfs/main.go
@@ -417,9 +417,10 @@ func commandShouldRunOnDaemon(details cmdDetails, req cmds.Request, root *cmds.C
 		return nil, err
 	}
 
-	if client != nil { // api file exists
+	if client != nil {
 		if details.cannotRunOnDaemon {
 			// check if daemon locked. legacy error text, for now.
+			log.Debugf("Command cannot run on daemon. Checking if daemon is locked")
 			if daemonLocked, _ := fsrepo.LockedByOtherProcess(req.InvocContext().ConfigRoot); daemonLocked {
 				return nil, cmds.ClientError("ipfs daemon is running. please stop it to run this command")
 			}
diff --git a/core/commands/repo.go b/core/commands/repo.go
index ff4615ef7..2aaadb67d 100644
--- a/core/commands/repo.go
+++ b/core/commands/repo.go
@@ -5,8 +5,12 @@ import (
 	"fmt"
 	cmds "github.com/ipfs/go-ipfs/commands"
 	corerepo "github.com/ipfs/go-ipfs/core/corerepo"
+	config "github.com/ipfs/go-ipfs/repo/config"
+	lockfile "github.com/ipfs/go-ipfs/repo/fsrepo/lock"
 	u "gx/ipfs/QmZNVWh8LLjAavuQ2JXuFmuYH3C11xo988vSgp7UQrTRj1/go-ipfs-util"
 	"io"
+	"os"
+	"path/filepath"
 )
 
 var RepoCmd = &cmds.Command{
@@ -20,6 +24,7 @@ var RepoCmd = &cmds.Command{
 	Subcommands: map[string]*cmds.Command{
 		"gc":   repoGcCmd,
 		"stat": repoStatCmd,
+		"fsck": RepoFsckCmd,
 	},
 }
 
@@ -32,7 +37,6 @@ set of stored objects and remove ones that are not pinned in
 order to reclaim hard disk space.
 `,
 	},
-
 	Options: []cmds.Option{
 		cmds.BoolOption("quiet", "q", "Write minimal output."),
 	},
@@ -152,3 +156,55 @@ RepoSize        int Size in bytes that the repo is currently taking.
 		},
 	},
 }
+
+var RepoFsckCmd = &cmds.Command{
+	Helptext: cmds.HelpText{
+		Tagline: "Removes repo lockfiles",
+		ShortDescription: `
+'ipfs repo fsck' is a plumbing command that will remove repo and level db
+lockfiles, as well as the api file. This command can only run when no ipfs
+daemons are running.
+`,
+	},
+	Run: func(req cmds.Request, res cmds.Response) {
+		configRoot := req.InvocContext().ConfigRoot
+
+		dsPath, err := config.DataStorePath(configRoot)
+		if err != nil {
+			res.SetError(err, cmds.ErrNormal)
+			return
+		}
+
+		dsLockFile := filepath.Join(dsPath, "LOCK") // TODO: get this lockfile programmatically
+		repoLockFile := filepath.Join(configRoot, lockfile.LockFile)
+		apiFile := filepath.Join(configRoot, "api") // TODO: get this programmatically
+
+		log.Infof("Removing repo lockfile: %s", repoLockFile)
+		log.Infof("Removing datastore lockfile: %s", dsLockFile)
+		log.Infof("Removing api file: %s", apiFile)
+
+		err = os.Remove(repoLockFile)
+		if err != nil && !os.IsNotExist(err) {
+			res.SetError(err, cmds.ErrNormal)
+			return
+		}
+		err = os.Remove(dsLockFile)
+		if err != nil && !os.IsNotExist(err) {
+			res.SetError(err, cmds.ErrNormal)
+			return
+		}
+		err = os.Remove(apiFile)
+		if err != nil && !os.IsNotExist(err) {
+			res.SetError(err, cmds.ErrNormal)
+			return
+		}
+
+		s := "Lockfiles have been removed."
+		log.Info(s)
+		res.SetOutput(&MessageOutput{s + "\n"})
+	},
+	Type: MessageOutput{},
+	Marshalers: cmds.MarshalerMap{
+		cmds.Text: MessageTextMarshaler,
+	},
+}
diff --git a/repo/fsrepo/fsrepo.go b/repo/fsrepo/fsrepo.go
index 9dcfb86ff..ee86a41f3 100644
--- a/repo/fsrepo/fsrepo.go
+++ b/repo/fsrepo/fsrepo.go
@@ -259,8 +259,11 @@ func Remove(repoPath string) error {
 // process. If true, then the repo cannot be opened by this process.
 func LockedByOtherProcess(repoPath string) (bool, error) {
 	repoPath = filepath.Clean(repoPath)
-	// NB: the lock is only held when repos are Open
-	return lockfile.Locked(repoPath)
+	locked, err := lockfile.Locked(repoPath)
+	if locked {
+		log.Debugf("(%t)<->Lock is held at %s", locked, repoPath)
+	}
+	return locked, err
 }
 
 // APIAddr returns the registered API addr, according to the api file
@@ -360,7 +363,7 @@ func (r *FSRepo) Close() error {
 	}
 
 	err := os.Remove(filepath.Join(r.path, apiFile))
-	if err != nil {
+	if err != nil && !os.IsNotExist(err) {
 		log.Warning("error removing api file: ", err)
 	}
 
diff --git a/repo/fsrepo/lock/lock.go b/repo/fsrepo/lock/lock.go
index 34f2d2339..f53703aff 100644
--- a/repo/fsrepo/lock/lock.go
+++ b/repo/fsrepo/lock/lock.go
@@ -10,12 +10,16 @@ import (
 
 	lock "github.com/ipfs/go-ipfs/Godeps/_workspace/src/github.com/camlistore/lock"
 	"gx/ipfs/QmZNVWh8LLjAavuQ2JXuFmuYH3C11xo988vSgp7UQrTRj1/go-ipfs-util"
+	logging "gx/ipfs/Qmazh5oNUVsDZTs2g59rq8aYQqwpss8tcUWQzor5sCCEuH/go-log"
 )
 
 // LockFile is the filename of the repo lock, relative to config dir
 // TODO rename repo lock and hide name
 const LockFile = "repo.lock"
 
+// log is the fsrepo logger
+var log = logging.Logger("lock")
+
 func errPerm(path string) error {
 	return fmt.Errorf("failed to take lock at %s: permission denied", path)
 }
@@ -26,29 +30,36 @@ func Lock(confdir string) (io.Closer, error) {
 }
 
 func Locked(confdir string) (bool, error) {
+	log.Debugf("Checking lock")
 	if !util.FileExists(path.Join(confdir, LockFile)) {
+		log.Debugf("File doesn't exist: %s", path.Join(confdir, LockFile))
 		return false, nil
 	}
 	if lk, err := Lock(confdir); err != nil {
 		// EAGAIN == someone else has the lock
 		if err == syscall.EAGAIN {
+			log.Debugf("Someone else has the lock: %s", path.Join(confdir, LockFile))
 			return true, nil
 		}
 		if strings.Contains(err.Error(), "can't Lock file") {
+			log.Debugf("Can't lock file: %s.\n reason: %s", path.Join(confdir, LockFile), err.Error())
 			return true, nil
 		}
 
 		// lock fails on permissions error
 		if os.IsPermission(err) {
+			log.Debugf("Lock fails on permissions error")
 			return false, errPerm(confdir)
 		}
 		if isLockCreatePermFail(err) {
+			log.Debugf("Lock fails on permissions error")
 			return false, errPerm(confdir)
 		}
 
 		// otherwise, we cant guarantee anything, error out
 		return false, err
 	} else {
+		log.Debugf("No one has a lock")
 		lk.Close()
 		return false, nil
 	}
diff --git a/test/sharness/t0083-repo-fsck.sh b/test/sharness/t0083-repo-fsck.sh
new file mode 100755
index 000000000..b53f846ab
--- /dev/null
+++ b/test/sharness/t0083-repo-fsck.sh
@@ -0,0 +1,190 @@
+#!/bin/sh
+#
+# Copyright (c) 2016 Mike Pfister 
+# MIT Licensed; see the LICENSE file in this repository.
+#
+
+test_description="Test ipfs repo fsck operations"
+
+. lib/test-lib.sh
+
+test_init_ipfs
+
+#############################
+# Test without daemon running
+############################# 
+# Note: if api file isn't present we can assume the daemon isn't running
+
+# Try with all lock files present: repo.lock, api, and datastore/LOCK with
+# repo.lock and datastore/LOCK being empty
+test_expect_success "'ipfs repo fsck' succeeds with no daemon running empty
+repo.lock" '
+    mkdir -p $IPFS_PATH &&
+    mkdir -p $IPFS_PATH/datastore &&
+    touch $IPFS_PATH/datastore/LOCK &&
+    touch $IPFS_PATH/repo.lock &&
+    printf "/ip4/127.0.0.1/tcp/5001" > $IPFS_PATH/api &&
+    ipfs repo fsck > fsck_out_actual1
+'
+test_expect_success "'ipfs repo fsck' output looks good with no daemon" '
+  grep "Lockfiles have been removed." fsck_out_actual1
+'
+
+# Make sure the files are actually removed
+test_expect_success "'ipfs repo fsck' confirm file deletion" '
+  test ! -e "$IPFS_PATH/repo.lock" &&
+  test ! -e "$IPFS_PATH/datastore/LOCK" &&
+  test ! -e "$IPFS_PATH/api"
+'
+
+# Try with all lock files present: repo.lock, api, and datastore/LOCK with
+# repo.lock is non-zero TODO: this test is broken until we find consensus on the
+# non-zero repo.lock issue
+test_expect_success "'ipfs repo fsck' succeeds with no daemon running non-zero
+repo.lock" '
+    mkdir -p $IPFS_PATH &&
+    printf ":D" > $IPFS_PATH/repo.lock &&
+    touch $IPFS_PATH/datastore/LOCK &&
+    ipfs repo fsck > fsck_out_actual1b
+'
+test_expect_success "'ipfs repo fsck' output looks good with no daemon" '
+  grep "Lockfiles have been removed." fsck_out_actual1b
+'
+
+# Make sure the files are actually removed
+test_expect_success "'ipfs repo fsck' confirm file deletion" '
+  test ! -e "$IPFS_PATH/repo.lock" &&
+  test ! -e "$IPFS_PATH/datastore/LOCK" &&
+  test ! -e "$IPFS_PATH/api"
+'
+
+########################
+# Test for partial locks
+######################## 
+
+# Try with locks api and datastore/LOCK
+test_expect_success "'ipfs repo fsck' succeeds partial lock" '
+    printf  "/ip4/127.0.0.1/tcp/5001" > $IPFS_PATH/api &&
+    touch $IPFS_PATH/datastore/LOCK &&
+    ipfs repo fsck > fsck_out_actual2
+'
+
+test_expect_success "'ipfs repo fsck' output looks good with no daemon" '
+  grep "Lockfiles have been removed." fsck_out_actual2
+'
+
+# Make sure the files are actually removed
+test_expect_success "'ipfs repo fsck' confirm file deletion" '
+  test ! -e "$IPFS_PATH/repo.lock" &&
+  test ! -e "$IPFS_PATH/datastore/LOCK" &&
+  test ! -e "$IPFS_PATH/api"
+'
+
+# Try with locks api and repo.lock
+test_expect_success "'ipfs repo fsck' succeeds partial lock" '
+    printf  "/ip4/127.0.0.1/tcp/5001" > $IPFS_PATH/api &&
+    touch $IPFS_PATH/repo.lock &&
+    ipfs repo fsck > fsck_out_actual3
+'
+
+test_expect_success "'ipfs repo fsck' output looks good with no daemon" '
+  grep "Lockfiles have been removed." fsck_out_actual3
+'
+
+# Make sure the files are actually removed
+test_expect_success "'ipfs repo fsck' confirm file deletion" '
+  test ! -e "$IPFS_PATH/repo.lock" &&
+  test ! -e "$IPFS_PATH/datastore/LOCK" &&
+  test ! -e "$IPFS_PATH/api"
+'
+
+# Try with locks repo.lock and datastore
+test_expect_success "'ipfs repo fsck' succeeds partial lock" '
+    touch $IPFS_PATH/repo.lock &&
+    touch $IPFS_PATH/datastore/LOCK &&
+    ipfs repo fsck > fsck_out_actual4
+'
+
+test_expect_success "'ipfs repo fsck' output looks good with no daemon" '
+  grep "Lockfiles have been removed." fsck_out_actual4
+'
+
+# Make sure the files are actually removed
+test_expect_success "'ipfs repo fsck' confirm file deletion" '
+  test ! -e "$IPFS_PATH/repo.lock" &&
+  test ! -e "$IPFS_PATH/datastore/LOCK" &&
+  test ! -e "$IPFS_PATH/api"
+'
+
+#######################
+# Test for single locks
+#######################
+
+# Try with single locks repo.lock
+test_expect_success "'ipfs repo fsck' succeeds partial lock" '
+    touch $IPFS_PATH/repo.lock &&
+    ipfs repo fsck > fsck_out_actual5
+'
+test_expect_success "'ipfs repo fsck' output looks good with no daemon" '
+  grep "Lockfiles have been removed." fsck_out_actual5
+'
+
+# Make sure the files are actually removed
+test_expect_success "'ipfs repo fsck' confirm file deletion" '
+  test ! -e "$IPFS_PATH/repo.lock" &&
+  test ! -e "$IPFS_PATH/datastore/LOCK" &&
+  test ! -e "$IPFS_PATH/api"
+'
+
+# Try with single locks datastore/LOCK
+test_expect_success "'ipfs repo fsck' succeeds partial lock" '
+    touch $IPFS_PATH/datastore/LOCK &&
+    ipfs repo fsck > fsck_out_actual6
+'
+test_expect_success "'ipfs repo fsck' output looks good with no daemon" '
+  grep "Lockfiles have been removed." fsck_out_actual6
+'
+
+# Make sure the files are actually removed
+test_expect_success "'ipfs repo fsck' confirm file deletion" '
+  test ! -e "$IPFS_PATH/repo.lock" &&
+  test ! -e "$IPFS_PATH/datastore/LOCK" &&
+  test ! -e "$IPFS_PATH/api"
+'
+
+# Try with single lock api
+test_expect_success "'ipfs repo fsck' succeeds partial lock" '
+  printf "/ip4/127.0.0.1/tcp/5001" > $IPFS_PATH/api &&
+  ipfs repo fsck > fsck_out_actual7
+'
+
+test_expect_success "'ipfs repo fsck' output looks good with no daemon" '
+  grep "Lockfiles have been removed." fsck_out_actual7
+'
+
+# Make sure the files are actually removed
+test_expect_success "'ipfs repo fsck' confirm file deletion" '
+  test ! -e "$IPFS_PATH/repo.lock" &&
+  test ! -e "$IPFS_PATH/datastore/LOCK" &&
+  test ! -e "$IPFS_PATH/api"
+'
+
+##########################
+# Test with daemon running
+########################## 
+
+test_launch_ipfs_daemon
+
+# Daemon is running -> command doesn't run
+test_expect_success "'ipfs repo fsck' fails with daemon running" '
+  ! (ipfs repo fsck 2>fsck_out_actual8 )
+
+'
+
+test_expect_success "'ipfs repo fsck' output looks good with daemon" '
+  grep "Error: ipfs daemon is running" fsck_out_actual8
+'
+
+test_kill_ipfs_daemon
+
+test_done