diff --git a/Assistant/Threads/SanityChecker.hs b/Assistant/Threads/SanityChecker.hs
index 446ade54f1..8aa691cdc9 100644
--- a/Assistant/Threads/SanityChecker.hs
+++ b/Assistant/Threads/SanityChecker.hs
@@ -16,6 +16,7 @@ import Assistant.DaemonStatus
 import Assistant.Alert
 import Assistant.Repair
 import Assistant.Ssh
+import qualified Annex.Branch
 import qualified Git.LsFiles
 import qualified Git.Command
 import qualified Git.Config
@@ -53,6 +54,12 @@ sanityCheckerStartupThread startupdelay = namedThreadUnchecked "SanityCheckerSta
 			debug ["no index file; restaging"]
 			modifyDaemonStatus_ $ \s -> s { forceRestage = True }
 		)
+	{- If the git-annex index file is corrupt, it's ok to remove it;
+	 - the data from the git-annex branch will be used, and the index
+	 - will be automatically regenerated. -}
+	unlessM (liftAnnex $ Annex.Branch.withIndex $ inRepo $ Git.Repair.checkIndexFast) $ do
+		notice ["corrupt annex/index file found at startup; removing"]
+		liftAnnex $ liftIO . nukeFile =<< fromRepo gitAnnexIndex
 
 	{- Fix up ssh remotes set up by past versions of the assistant. -}
 	liftIO $ fixUpSshRemotes
diff --git a/debian/changelog b/debian/changelog
index f1d76b7815..8a9f57be34 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -13,6 +13,8 @@ git-annex (5.20140108) UNRELEASED; urgency=medium
     environment. This typically resulted in git-annex branch log files being
     committed to the master branch and later showing up in the work tree.
     (These log files can be safely removed.)
+  * assistant: Detect if .git/annex/index is corrupt at startup, and
+    recover.
 
  -- Joey Hess <joeyh@debian.org>  Wed, 08 Jan 2014 13:13:54 -0400
 
diff --git a/doc/bugs/index_file_smaller_than_expected.mdwn b/doc/bugs/index_file_smaller_than_expected.mdwn
index b82bd62b3a..0eac3f20ea 100644
--- a/doc/bugs/index_file_smaller_than_expected.mdwn
+++ b/doc/bugs/index_file_smaller_than_expected.mdwn
@@ -48,3 +48,6 @@ NetWatcherFallback crashed: user error (git ["--git-dir=/Users/juh/Share/.git","
 
 # End of transcript or log.
 """]]
+
+> Made assistant detect corrupted .git/annex/index on startup and correct
+> it. [[fixed|done]] --[[Joey]]