diff --git a/.git-annex/uuid.log b/.git-annex/uuid.log
deleted file mode 100644
index 8cd9452b64..0000000000
--- a/.git-annex/uuid.log
+++ /dev/null
@@ -1 +0,0 @@
-1ac368a4-19e2-11e0-8c0f-8fcd42cf5a8d test repo
diff --git a/Command.hs b/Command.hs
index 0bbc6088c5..601b584642 100644
--- a/Command.hs
+++ b/Command.hs
@@ -147,7 +147,7 @@ withStrings a params = return $ map a params
 withFilesToBeCommitted :: CommandSeekStrings
 withFilesToBeCommitted a params = do
 	repo <- Annex.gitRepo
-	tocommit <- liftIO $ runPreserveOrder (Git.stagedFiles repo) params
+	tocommit <- liftIO $ runPreserveOrder (Git.stagedFilesNotDeleted repo) params
 	tocommit' <- filterFiles tocommit
 	return $ map a tocommit'
 withFilesUnlocked :: CommandSeekBackendFiles
diff --git a/Command/Unannex.hs b/Command/Unannex.hs
index 3810cca1c2..c663b29ab0 100644
--- a/Command/Unannex.hs
+++ b/Command/Unannex.hs
@@ -8,6 +8,7 @@
 module Command.Unannex where
 
 import Control.Monad.State (liftIO)
+import Control.Monad (unless)
 import System.Directory
 
 import Command
@@ -32,6 +33,11 @@ start file = isAnnexed file $ \(key, backend) -> do
 	ishere <- inAnnex key
 	if ishere
 		then do
+			g <- Annex.gitRepo
+			staged <- liftIO $ Git.stagedFiles g [Git.workTree g]
+			unless (null staged) $
+				error "This command cannot be run when there are already files staged for commit."
+
 			showStart "unannex" file
 			return $ Just $ perform file key backend
 		else return Nothing
diff --git a/GitRepo.hs b/GitRepo.hs
index 4e69544d43..031a9cbe21 100644
--- a/GitRepo.hs
+++ b/GitRepo.hs
@@ -38,6 +38,7 @@ module GitRepo (
 	inRepo,
 	notInRepo,
 	stagedFiles,
+	stagedFilesNotDeleted,
 	changedUnstagedFiles,
 	checkAttr,
 	decodeGitFile,
@@ -243,12 +244,20 @@ notInRepo :: Repo -> [FilePath] -> IO [FilePath]
 notInRepo repo l = pipeNullSplit repo $
 	["ls-files", "--others", "--exclude-standard", "-z", "--"] ++ l
 
+{- Returns a list of all files that are staged for commit. -}
+stagedFiles :: Repo -> [FilePath] -> IO [FilePath]
+stagedFiles repo l = stagedFiles' repo l []
+
 {- Returns a list of the files, staged for commit, that are being added,
  - moved, or changed (but not deleted), from the specified locations. -}
-stagedFiles :: Repo -> [FilePath] -> IO [FilePath]
-stagedFiles repo l = pipeNullSplit repo $
-	["diff", "--cached", "--name-only", "--diff-filter=ACMRT", "-z", 
-		"--"] ++ l
+stagedFilesNotDeleted :: Repo -> [FilePath] -> IO [FilePath]
+stagedFilesNotDeleted repo l = stagedFiles' repo l ["--diff-filter=ACMRT"]
+
+stagedFiles' :: Repo -> [FilePath] -> [String] -> IO [FilePath]
+stagedFiles' repo l middle = pipeNullSplit repo $ start ++ middle ++ end
+	where
+		start = ["diff", "--cached", "--name-only", "-z"]
+		end = ["--"] ++ l
 
 {- Returns a list of files that have unstaged changes. -}
 changedUnstagedFiles :: Repo -> [FilePath] -> IO [FilePath]