diff --git a/src/libexpr/primops/fetchMercurial.cc b/src/libexpr/primops/fetchMercurial.cc
index 2a423f61b..7def7103b 100644
--- a/src/libexpr/primops/fetchMercurial.cc
+++ b/src/libexpr/primops/fetchMercurial.cc
@@ -47,11 +47,15 @@ HgInfo exportMercurial(ref<Store> store, const std::string & uri,
 
             PathFilter filter = [&](const Path & p) -> bool {
                 assert(hasPrefix(p, uri));
-                auto st = lstat(p);
                 std::string file(p, uri.size() + 1);
-                if (file == ".hg") return false;
-                // FIXME: filter out directories with no tracked files.
-                if (S_ISDIR(st.st_mode)) return true;
+
+                auto st = lstat(p);
+
+                if (S_ISDIR(st.st_mode)) {
+                    auto i = files.lower_bound(file);
+                    return i != files.end() && hasPrefix(*i, file);
+                }
+
                 return files.count(file);
             };
 
diff --git a/src/libexpr/primops/fetchgit.cc b/src/libexpr/primops/fetchgit.cc
index 1d8f55bcd..baa48f642 100644
--- a/src/libexpr/primops/fetchgit.cc
+++ b/src/libexpr/primops/fetchgit.cc
@@ -44,11 +44,15 @@ GitInfo exportGit(ref<Store> store, const std::string & uri,
 
             PathFilter filter = [&](const Path & p) -> bool {
                 assert(hasPrefix(p, uri));
-                auto st = lstat(p);
                 std::string file(p, uri.size() + 1);
-                if (file == ".git") return false;
-                // FIXME: filter out directories with no tracked files.
-                if (S_ISDIR(st.st_mode)) return true;
+
+                auto st = lstat(p);
+
+                if (S_ISDIR(st.st_mode)) {
+                    auto i = files.lower_bound(file);
+                    return i != files.end() && hasPrefix(*i, file);
+                }
+
                 return files.count(file);
             };
 
diff --git a/tests/fetchGit.sh b/tests/fetchGit.sh
index e2bb7b68c..a967380cd 100644
--- a/tests/fetchGit.sh
+++ b/tests/fetchGit.sh
@@ -57,15 +57,18 @@ path2=$(nix eval --raw "(builtins.fetchGit $repo).outPath")
 [[ $path = $path2 ]]
 
 # Using an unclean tree should yield the tracked but uncommitted changes.
-echo foo > $repo/foo
+mkdir $repo/dir1 $repo/dir2
+echo foo > $repo/dir1/foo
 echo bar > $repo/bar
-git -C $repo add foo
+echo bar > $repo/dir2/bar
+git -C $repo add dir1/foo
 git -C $repo rm hello
 
 path2=$(nix eval --raw "(builtins.fetchGit $repo).outPath")
 [ ! -e $path2/hello ]
 [ ! -e $path2/bar ]
-[[ $(cat $path2/foo) = foo ]]
+[ ! -e $path2/dir2/bar ]
+[[ $(cat $path2/dir1/foo) = foo ]]
 
 [[ $(nix eval --raw "(builtins.fetchGit $repo).rev") = 0000000000000000000000000000000000000000 ]]
 
diff --git a/tests/fetchMercurial.sh b/tests/fetchMercurial.sh
index 9c897ada9..0c9f4bdbb 100644
--- a/tests/fetchMercurial.sh
+++ b/tests/fetchMercurial.sh
@@ -58,15 +58,18 @@ path2=$(nix eval --raw "(builtins.fetchMercurial $repo).outPath")
 [[ $path = $path2 ]]
 
 # Using an unclean tree should yield the tracked but uncommitted changes.
-echo foo > $repo/foo
+mkdir $repo/dir1 $repo/dir2
+echo foo > $repo/dir1/foo
 echo bar > $repo/bar
-hg add --cwd $repo foo
+echo bar > $repo/dir2/bar
+hg add --cwd $repo dir1/foo
 hg rm --cwd $repo hello
 
 path2=$(nix eval --raw "(builtins.fetchMercurial $repo).outPath")
 [ ! -e $path2/hello ]
 [ ! -e $path2/bar ]
-[[ $(cat $path2/foo) = foo ]]
+[ ! -e $path2/dir2/bar ]
+[[ $(cat $path2/dir1/foo) = foo ]]
 
 [[ $(nix eval --raw "(builtins.fetchMercurial $repo).rev") = 0000000000000000000000000000000000000000 ]]