diff --git a/builtin/clone.c b/builtin/clone.c
index 5c439f1394c9a0..0702b0e9d025bc 100644
--- a/builtin/clone.c
+++ b/builtin/clone.c
@@ -747,6 +747,7 @@ static int checkout(int submodule_progress)
 	memset(&opts, 0, sizeof opts);
 	opts.update = 1;
 	opts.merge = 1;
+	opts.clone = 1;
 	opts.fn = oneway_merge;
 	opts.verbose_update = (option_verbosity >= 0);
 	opts.src_index = &the_index;
diff --git a/cache.h b/cache.h
index 8b447652a7e94a..6d6138f4f1cb8e 100644
--- a/cache.h
+++ b/cache.h
@@ -1455,6 +1455,7 @@ struct checkout {
 	unsigned force:1,
 		 quiet:1,
 		 not_new:1,
+		 clone:1,
 		 refresh_cache:1;
 };
 #define CHECKOUT_INIT { NULL, "" }
diff --git a/entry.c b/entry.c
index b5d1d3cf2312f6..2bce133521e896 100644
--- a/entry.c
+++ b/entry.c
@@ -399,6 +399,31 @@ static int check_path(const char *path, int len, struct stat *st, int skiplen)
 	return lstat(path, st);
 }
 
+static void mark_colliding_entries(const struct checkout *state,
+				   struct cache_entry *ce, struct stat *st)
+{
+#if !defined(GIT_WINDOWS_NATIVE) /* inode is always zero on Windows */
+	int i;
+
+	for (i = 0; i < state->istate->cache_nr; i++) {
+		struct cache_entry *dup = state->istate->cache[i];
+
+		if (dup == ce)
+			break;
+
+		if (dup->ce_flags & (CE_MATCHED | CE_VALID | CE_SKIP_WORKTREE))
+			continue;
+
+		if (dup->ce_stat_data.sd_ino == st->st_ino) {
+			dup->ce_flags |= CE_MATCHED;
+			break;
+		}
+	}
+#endif
+
+	ce->ce_flags |= CE_MATCHED;
+}
+
 /*
  * Write the contents from ce out to the working tree.
  *
@@ -455,6 +480,9 @@ int checkout_entry(struct cache_entry *ce,
 			return -1;
 		}
 
+		if (state->clone)
+			mark_colliding_entries(state, ce, &st);
+
 		/*
 		 * We unlink the old file, to get the new one with the
 		 * right permissions (including umask, which is nasty
diff --git a/t/t5601-clone.sh b/t/t5601-clone.sh
index 0b620377448bc3..f2eb73bc74ae70 100755
--- a/t/t5601-clone.sh
+++ b/t/t5601-clone.sh
@@ -624,10 +624,16 @@ test_expect_success 'clone on case-insensitive fs' '
 			git hash-object -w -t tree --stdin) &&
 		c=$(git commit-tree -m bogus $t) &&
 		git update-ref refs/heads/bogus $c &&
-		git clone -b bogus . bogus
+		git clone -b bogus . bogus 2>warning
 	)
 '
 
+test_expect_success !MINGW,!CYGWIN,CASE_INSENSITIVE_FS 'colliding file detection' '
+	grep X icasefs/warning &&
+	grep x icasefs/warning &&
+	test_i18ngrep "the following paths have collided" icasefs/warning
+'
+
 partial_clone () {
 	       SERVER="$1" &&
 	       URL="$2" &&
diff --git a/unpack-trees.c b/unpack-trees.c
index cd0680f11e3580..cc36f82fdedfd7 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -359,6 +359,12 @@ static int check_updates(struct unpack_trees_options *o)
 	state.refresh_cache = 1;
 	state.istate = index;
 
+	if (o->clone) {
+		state.clone = 1;
+		for (i = 0; i < index->cache_nr; i++)
+			index->cache[i]->ce_flags &= ~CE_MATCHED;
+	}
+
 	progress = get_progress(o);
 
 	if (o->update)
@@ -423,6 +429,28 @@ static int check_updates(struct unpack_trees_options *o)
 	errs |= finish_delayed_checkout(&state);
 	if (o->update)
 		git_attr_set_direction(GIT_ATTR_CHECKIN, NULL);
+
+	if (o->clone) {
+		int printed_warning = 0;
+
+		for (i = 0; i < index->cache_nr; i++) {
+			struct cache_entry *ce = index->cache[i];
+
+			if (!(ce->ce_flags & CE_MATCHED))
+				continue;
+
+			if (!printed_warning) {
+				warning(_("the following paths have collided (e.g. case-sensitive paths\n"
+					  "on a case-insensitive filesystem) and only one from the same\n"
+					  "colliding group is in the working tree:\n"));
+				printed_warning = 1;
+			}
+
+			fprintf(stderr, "  '%s'\n", ce->name);
+			ce->ce_flags &= ~CE_MATCHED;
+		}
+	}
+
 	return errs != 0;
 }
 
diff --git a/unpack-trees.h b/unpack-trees.h
index c2b434c60648fb..d940f1c5c287a7 100644
--- a/unpack-trees.h
+++ b/unpack-trees.h
@@ -42,6 +42,7 @@ struct unpack_trees_options {
 	unsigned int reset,
 		     merge,
 		     update,
+		     clone,
 		     index_only,
 		     nontrivial_merge,
 		     trivial_merges_only,