diff --git a/git-filter-branch.sh b/git-filter-branch.sh
index 49e13f0bb1..010353ad82 100755
--- a/git-filter-branch.sh
+++ b/git-filter-branch.sh
@@ -252,7 +252,16 @@ while read commit parents; do
 		git read-tree -i -m $commit
 		;;
 	*)
-		git read-tree -i -m $commit:"$filter_subdir"
+		# The commit may not have the subdirectory at all
+		err=$(git read-tree -i -m $commit:"$filter_subdir" 2>&1) || {
+			if ! git rev-parse --verify $commit:"$filter_subdir" 2>/dev/null
+			then
+				rm -f "$GIT_INDEX_FILE"
+			else
+				echo >&2 "$err"
+				false
+			fi
+		}
 	esac || die "Could not initialize the index"
 
 	GIT_COMMIT=$commit
diff --git a/t/t7003-filter-branch.sh b/t/t7003-filter-branch.sh
index 868babc4b2..6e14bf1c7f 100755
--- a/t/t7003-filter-branch.sh
+++ b/t/t7003-filter-branch.sh
@@ -179,4 +179,28 @@ test_expect_success 'Name needing quotes' '
 
 '
 
+test_expect_success 'Subdirectory filter with disappearing trees' '
+	git reset --hard &&
+	git checkout master &&
+
+	mkdir foo &&
+	touch foo/bar &&
+	git add foo &&
+	test_tick &&
+	git commit -m "Adding foo" &&
+
+	git rm -r foo &&
+	test_tick &&
+	git commit -m "Removing foo" &&
+
+	mkdir foo &&
+	touch foo/bar &&
+	git add foo &&
+	test_tick &&
+	git commit -m "Re-adding foo" &&
+
+	git filter-branch -f --subdirectory-filter foo &&
+	test $(git rev-list master | wc -l) = 3
+'
+
 test_done