diff --git a/Documentation/git-rm.txt b/Documentation/git-rm.txt
index 5d31860eb1..882cb1171b 100644
--- a/Documentation/git-rm.txt
+++ b/Documentation/git-rm.txt
@@ -107,6 +107,21 @@ as well as modifications of existing paths.
 Typically you would first remove all tracked files from the working
 tree using this command:
 
+Submodules
+~~~~~~~~~~
+Only submodules using a gitfile (which means they were cloned
+with a git version 1.7.8 or newer) will be removed from the work
+tree, as their repository lives inside the .git directory of the
+superproject. If a submodule (or one of those nested inside it)
+still uses a .git directory, `git rm` will fail - no matter if forced
+or not - to protect the submodule's history.
+
+A submodule is considered up-to-date when the HEAD is the same as
+recorded in the index, no tracked files are modified and no untracked
+files that aren't ignored are present in the submodules work tree.
+Ignored files are deemed expendable and won't stop a submodule's work
+tree from being removed.
+
 ----------------
 git ls-files -z | xargs -0 rm -f
 ----------------
diff --git a/builtin/rm.c b/builtin/rm.c
index b384c4c3cf..2aea3b5653 100644
--- a/builtin/rm.c
+++ b/builtin/rm.c
@@ -9,6 +9,7 @@
 #include "cache-tree.h"
 #include "tree-walk.h"
 #include "parse-options.h"
+#include "submodule.h"
 
 static const char * const builtin_rm_usage[] = {
 	N_("git rm [options] [--] <file>..."),
@@ -17,9 +18,58 @@ static const char * const builtin_rm_usage[] = {
 
 static struct {
 	int nr, alloc;
-	const char **name;
+	struct {
+		const char *name;
+		char is_submodule;
+	} *entry;
 } list;
 
+static int get_ours_cache_pos(const char *path, int pos)
+{
+	int i = -pos - 1;
+
+	while ((i < active_nr) && !strcmp(active_cache[i]->name, path)) {
+		if (ce_stage(active_cache[i]) == 2)
+			return i;
+		i++;
+	}
+	return -1;
+}
+
+static int check_submodules_use_gitfiles(void)
+{
+	int i;
+	int errs = 0;
+
+	for (i = 0; i < list.nr; i++) {
+		const char *name = list.entry[i].name;
+		int pos;
+		struct cache_entry *ce;
+		struct stat st;
+
+		pos = cache_name_pos(name, strlen(name));
+		if (pos < 0) {
+			pos = get_ours_cache_pos(name, pos);
+			if (pos < 0)
+				continue;
+		}
+		ce = active_cache[pos];
+
+		if (!S_ISGITLINK(ce->ce_mode) ||
+		    (lstat(ce->name, &st) < 0) ||
+		    is_empty_dir(name))
+			continue;
+
+		if (!submodule_uses_gitfile(name))
+			errs = error(_("submodule '%s' (or one of its nested "
+				     "submodules) uses a .git directory\n"
+				     "(use 'rm -rf' if you really want to remove "
+				     "it including all of its history)"), name);
+	}
+
+	return errs;
+}
+
 static int check_local_mod(unsigned char *head, int index_only)
 {
 	/*
@@ -37,15 +87,26 @@ static int check_local_mod(unsigned char *head, int index_only)
 		struct stat st;
 		int pos;
 		struct cache_entry *ce;
-		const char *name = list.name[i];
+		const char *name = list.entry[i].name;
 		unsigned char sha1[20];
 		unsigned mode;
 		int local_changes = 0;
 		int staged_changes = 0;
 
 		pos = cache_name_pos(name, strlen(name));
-		if (pos < 0)
-			continue; /* removing unmerged entry */
+		if (pos < 0) {
+			/*
+			 * Skip unmerged entries except for populated submodules
+			 * that could lose history when removed.
+			 */
+			pos = get_ours_cache_pos(name, pos);
+			if (pos < 0)
+				continue;
+
+			if (!S_ISGITLINK(active_cache[pos]->ce_mode) ||
+			    is_empty_dir(name))
+				continue;
+		}
 		ce = active_cache[pos];
 
 		if (lstat(ce->name, &st) < 0) {
@@ -58,9 +119,10 @@ static int check_local_mod(unsigned char *head, int index_only)
 			/* if a file was removed and it is now a
 			 * directory, that is the same as ENOENT as
 			 * far as git is concerned; we do not track
-			 * directories.
+			 * directories unless they are submodules.
 			 */
-			continue;
+			if (!S_ISGITLINK(ce->ce_mode))
+				continue;
 		}
 
 		/*
@@ -80,8 +142,11 @@ static int check_local_mod(unsigned char *head, int index_only)
 
 		/*
 		 * Is the index different from the file in the work tree?
+		 * If it's a submodule, is its work tree modified?
 		 */
-		if (ce_match_stat(ce, &st, 0))
+		if (ce_match_stat(ce, &st, 0) ||
+		    (S_ISGITLINK(ce->ce_mode) &&
+		     !ok_to_remove_submodule(ce->name)))
 			local_changes = 1;
 
 		/*
@@ -115,10 +180,18 @@ static int check_local_mod(unsigned char *head, int index_only)
 				errs = error(_("'%s' has changes staged in the index\n"
 					     "(use --cached to keep the file, "
 					     "or -f to force removal)"), name);
-			if (local_changes)
-				errs = error(_("'%s' has local modifications\n"
-					     "(use --cached to keep the file, "
-					     "or -f to force removal)"), name);
+			if (local_changes) {
+				if (S_ISGITLINK(ce->ce_mode) &&
+				    !submodule_uses_gitfile(name)) {
+					errs = error(_("submodule '%s' (or one of its nested "
+						     "submodules) uses a .git directory\n"
+						     "(use 'rm -rf' if you really want to remove "
+						     "it including all of its history)"), name);
+				} else
+					errs = error(_("'%s' has local modifications\n"
+						     "(use --cached to keep the file, "
+						     "or -f to force removal)"), name);
+			}
 		}
 	}
 	return errs;
@@ -173,8 +246,9 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 		struct cache_entry *ce = active_cache[i];
 		if (!match_pathspec(pathspec, ce->name, ce_namelen(ce), 0, seen))
 			continue;
-		ALLOC_GROW(list.name, list.nr + 1, list.alloc);
-		list.name[list.nr++] = ce->name;
+		ALLOC_GROW(list.entry, list.nr + 1, list.alloc);
+		list.entry[list.nr].name = ce->name;
+		list.entry[list.nr++].is_submodule = S_ISGITLINK(ce->ce_mode);
 	}
 
 	if (pathspec) {
@@ -215,6 +289,9 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 			hashclr(sha1);
 		if (check_local_mod(sha1, index_only))
 			exit(1);
+	} else if (!index_only) {
+		if (check_submodules_use_gitfiles())
+			exit(1);
 	}
 
 	/*
@@ -222,7 +299,7 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 	 * the index unless all of them succeed.
 	 */
 	for (i = 0; i < list.nr; i++) {
-		const char *path = list.name[i];
+		const char *path = list.entry[i].name;
 		if (!quiet)
 			printf("rm '%s'\n", path);
 
@@ -244,7 +321,25 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 	if (!index_only) {
 		int removed = 0;
 		for (i = 0; i < list.nr; i++) {
-			const char *path = list.name[i];
+			const char *path = list.entry[i].name;
+			if (list.entry[i].is_submodule) {
+				if (is_empty_dir(path)) {
+					if (!rmdir(path)) {
+						removed = 1;
+						continue;
+					}
+				} else {
+					struct strbuf buf = STRBUF_INIT;
+					strbuf_addstr(&buf, path);
+					if (!remove_dir_recursively(&buf, 0)) {
+						removed = 1;
+						strbuf_release(&buf);
+						continue;
+					}
+					strbuf_release(&buf);
+					/* Fallthrough and let remove_path() fail. */
+				}
+			}
 			if (!remove_path(path)) {
 				removed = 1;
 				continue;
diff --git a/submodule.c b/submodule.c
index 50f213e926..e3e0b455ea 100644
--- a/submodule.c
+++ b/submodule.c
@@ -759,6 +759,86 @@ unsigned is_submodule_modified(const char *path, int ignore_untracked)
 	return dirty_submodule;
 }
 
+int submodule_uses_gitfile(const char *path)
+{
+	struct child_process cp;
+	const char *argv[] = {
+		"submodule",
+		"foreach",
+		"--quiet",
+		"--recursive",
+		"test -f .git",
+		NULL,
+	};
+	struct strbuf buf = STRBUF_INIT;
+	const char *git_dir;
+
+	strbuf_addf(&buf, "%s/.git", path);
+	git_dir = read_gitfile(buf.buf);
+	if (!git_dir) {
+		strbuf_release(&buf);
+		return 0;
+	}
+	strbuf_release(&buf);
+
+	/* Now test that all nested submodules use a gitfile too */
+	memset(&cp, 0, sizeof(cp));
+	cp.argv = argv;
+	cp.env = local_repo_env;
+	cp.git_cmd = 1;
+	cp.no_stdin = 1;
+	cp.no_stderr = 1;
+	cp.no_stdout = 1;
+	cp.dir = path;
+	if (run_command(&cp))
+		return 0;
+
+	return 1;
+}
+
+int ok_to_remove_submodule(const char *path)
+{
+	struct stat st;
+	ssize_t len;
+	struct child_process cp;
+	const char *argv[] = {
+		"status",
+		"--porcelain",
+		"-u",
+		"--ignore-submodules=none",
+		NULL,
+	};
+	struct strbuf buf = STRBUF_INIT;
+	int ok_to_remove = 1;
+
+	if ((lstat(path, &st) < 0) || is_empty_dir(path))
+		return 1;
+
+	if (!submodule_uses_gitfile(path))
+		return 0;
+
+	memset(&cp, 0, sizeof(cp));
+	cp.argv = argv;
+	cp.env = local_repo_env;
+	cp.git_cmd = 1;
+	cp.no_stdin = 1;
+	cp.out = -1;
+	cp.dir = path;
+	if (start_command(&cp))
+		die("Could not run 'git status --porcelain -uall --ignore-submodules=none' in submodule %s", path);
+
+	len = strbuf_read(&buf, cp.out, 1024);
+	if (len > 2)
+		ok_to_remove = 0;
+	close(cp.out);
+
+	if (finish_command(&cp))
+		die("'git status --porcelain -uall --ignore-submodules=none' failed in submodule %s", path);
+
+	strbuf_release(&buf);
+	return ok_to_remove;
+}
+
 static int find_first_merges(struct object_array *result, const char *path,
 		struct commit *a, struct commit *b)
 {
diff --git a/submodule.h b/submodule.h
index 594b50d510..f2e8271fc6 100644
--- a/submodule.h
+++ b/submodule.h
@@ -28,6 +28,8 @@ int fetch_populated_submodules(const struct argv_array *options,
 			       const char *prefix, int command_line_option,
 			       int quiet);
 unsigned is_submodule_modified(const char *path, int ignore_untracked);
+int submodule_uses_gitfile(const char *path);
+int ok_to_remove_submodule(const char *path);
 int merge_submodule(unsigned char result[20], const char *path, const unsigned char base[20],
 		    const unsigned char a[20], const unsigned char b[20], int search);
 int find_unpushed_submodules(unsigned char new_sha1[20], const char *remotes_name,
diff --git a/t/t3600-rm.sh b/t/t3600-rm.sh
index 9fd28bcf34..97254e8d33 100755
--- a/t/t3600-rm.sh
+++ b/t/t3600-rm.sh
@@ -262,4 +262,347 @@ test_expect_success 'rm removes subdirectories recursively' '
 	! test -d dir
 '
 
+cat >expect <<EOF
+D  submod
+EOF
+
+cat >expect.modified <<EOF
+ M submod
+EOF
+
+test_expect_success 'rm removes empty submodules from work tree' '
+	mkdir submod &&
+	git update-index --add --cacheinfo 160000 $(git rev-parse HEAD) submod &&
+	git config -f .gitmodules submodule.sub.url ./. &&
+	git config -f .gitmodules submodule.sub.path submod &&
+	git submodule init &&
+	git add .gitmodules &&
+	git commit -m "add submodule" &&
+	git rm submod &&
+	test ! -e submod &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect actual
+'
+
+test_expect_success 'rm removes removed submodule from index' '
+	git reset --hard &&
+	git submodule update &&
+	rm -rf submod &&
+	git rm submod &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect actual
+'
+
+test_expect_success 'rm removes work tree of unmodified submodules' '
+	git reset --hard &&
+	git submodule update &&
+	git rm submod &&
+	test ! -d submod &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect actual
+'
+
+test_expect_success 'rm of a populated submodule with different HEAD fails unless forced' '
+	git reset --hard &&
+	git submodule update &&
+	(cd submod &&
+		git checkout HEAD^
+	) &&
+	test_must_fail git rm submod &&
+	test -d submod &&
+	test -f submod/.git &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect.modified actual &&
+	git rm -f submod &&
+	test ! -d submod &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect actual
+'
+
+test_expect_success 'rm of a populated submodule with modifications fails unless forced' '
+	git reset --hard &&
+	git submodule update &&
+	(cd submod &&
+		echo X >empty
+	) &&
+	test_must_fail git rm submod &&
+	test -d submod &&
+	test -f submod/.git &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect.modified actual &&
+	git rm -f submod &&
+	test ! -d submod &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect actual
+'
+
+test_expect_success 'rm of a populated submodule with untracked files fails unless forced' '
+	git reset --hard &&
+	git submodule update &&
+	(cd submod &&
+		echo X >untracked
+	) &&
+	test_must_fail git rm submod &&
+	test -d submod &&
+	test -f submod/.git &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect.modified actual &&
+	git rm -f submod &&
+	test ! -d submod &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect actual
+'
+
+test_expect_success 'setup submodule conflict' '
+	git reset --hard &&
+	git submodule update &&
+	git checkout -b branch1 &&
+	echo 1 >nitfol &&
+	git add nitfol &&
+	git commit -m "added nitfol 1" &&
+	git checkout -b branch2 master &&
+	echo 2 >nitfol &&
+	git add nitfol &&
+	git commit -m "added nitfol 2" &&
+	git checkout -b conflict1 master &&
+	(cd submod &&
+		git fetch &&
+		git checkout branch1
+	) &&
+	git add submod &&
+	git commit -m "submod 1" &&
+	git checkout -b conflict2 master &&
+	(cd submod &&
+		git checkout branch2
+	) &&
+	git add submod &&
+	git commit -m "submod 2"
+'
+
+cat >expect.conflict <<EOF
+UU submod
+EOF
+
+test_expect_success 'rm removes work tree of unmodified conflicted submodule' '
+	git checkout conflict1 &&
+	git reset --hard &&
+	git submodule update &&
+	test_must_fail git merge conflict2 &&
+	git rm submod &&
+	test ! -d submod &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect actual
+'
+
+test_expect_success 'rm of a conflicted populated submodule with different HEAD fails unless forced' '
+	git checkout conflict1 &&
+	git reset --hard &&
+	git submodule update &&
+	(cd submod &&
+		git checkout HEAD^
+	) &&
+	test_must_fail git merge conflict2 &&
+	test_must_fail git rm submod &&
+	test -d submod &&
+	test -f submod/.git &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect.conflict actual &&
+	git rm -f submod &&
+	test ! -d submod &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect actual
+'
+
+test_expect_success 'rm of a conflicted populated submodule with modifications fails unless forced' '
+	git checkout conflict1 &&
+	git reset --hard &&
+	git submodule update &&
+	(cd submod &&
+		echo X >empty
+	) &&
+	test_must_fail git merge conflict2 &&
+	test_must_fail git rm submod &&
+	test -d submod &&
+	test -f submod/.git &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect.conflict actual &&
+	git rm -f submod &&
+	test ! -d submod &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect actual
+'
+
+test_expect_success 'rm of a conflicted populated submodule with untracked files fails unless forced' '
+	git checkout conflict1 &&
+	git reset --hard &&
+	git submodule update &&
+	(cd submod &&
+		echo X >untracked
+	) &&
+	test_must_fail git merge conflict2 &&
+	test_must_fail git rm submod &&
+	test -d submod &&
+	test -f submod/.git &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect.conflict actual &&
+	git rm -f submod &&
+	test ! -d submod &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect actual
+'
+
+test_expect_success 'rm of a conflicted populated submodule with a .git directory fails even when forced' '
+	git checkout conflict1 &&
+	git reset --hard &&
+	git submodule update &&
+	(cd submod &&
+		rm .git &&
+		cp -a ../.git/modules/sub .git &&
+		GIT_WORK_TREE=. git config --unset core.worktree
+	) &&
+	test_must_fail git merge conflict2 &&
+	test_must_fail git rm submod &&
+	test -d submod &&
+	test -d submod/.git &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect.conflict actual &&
+	test_must_fail git rm -f submod &&
+	test -d submod &&
+	test -d submod/.git &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect.conflict actual &&
+	git merge --abort &&
+	rm -rf submod
+'
+
+test_expect_success 'rm of a conflicted unpopulated submodule succeeds' '
+	git checkout conflict1 &&
+	git reset --hard &&
+	test_must_fail git merge conflict2 &&
+	git rm submod &&
+	test ! -d submod &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect actual
+'
+
+test_expect_success 'rm of a populated submodule with a .git directory fails even when forced' '
+	git checkout -f master &&
+	git reset --hard &&
+	git submodule update &&
+	(cd submod &&
+		rm .git &&
+		cp -a ../.git/modules/sub .git &&
+		GIT_WORK_TREE=. git config --unset core.worktree
+	) &&
+	test_must_fail git rm submod &&
+	test -d submod &&
+	test -d submod/.git &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	! test -s actual &&
+	test_must_fail git rm -f submod &&
+	test -d submod &&
+	test -d submod/.git &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	! test -s actual &&
+	rm -rf submod
+'
+
+cat >expect.deepmodified <<EOF
+ M submod/subsubmod
+EOF
+
+test_expect_success 'setup subsubmodule' '
+	git reset --hard &&
+	git submodule update &&
+	(cd submod &&
+		git update-index --add --cacheinfo 160000 $(git rev-parse HEAD) subsubmod &&
+		git config -f .gitmodules submodule.sub.url ../. &&
+		git config -f .gitmodules submodule.sub.path subsubmod &&
+		git submodule init &&
+		git add .gitmodules &&
+		git commit -m "add subsubmodule" &&
+		git submodule update subsubmod
+	) &&
+	git commit -a -m "added deep submodule"
+'
+
+test_expect_success 'rm recursively removes work tree of unmodified submodules' '
+	git rm submod &&
+	test ! -d submod &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect actual
+'
+
+test_expect_success 'rm of a populated nested submodule with different nested HEAD fails unless forced' '
+	git reset --hard &&
+	git submodule update --recursive &&
+	(cd submod/subsubmod &&
+		git checkout HEAD^
+	) &&
+	test_must_fail git rm submod &&
+	test -d submod &&
+	test -f submod/.git &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect.modified actual &&
+	git rm -f submod &&
+	test ! -d submod &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect actual
+'
+
+test_expect_success 'rm of a populated nested submodule with nested modifications fails unless forced' '
+	git reset --hard &&
+	git submodule update --recursive &&
+	(cd submod/subsubmod &&
+		echo X >empty
+	) &&
+	test_must_fail git rm submod &&
+	test -d submod &&
+	test -f submod/.git &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect.modified actual &&
+	git rm -f submod &&
+	test ! -d submod &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect actual
+'
+
+test_expect_success 'rm of a populated nested submodule with nested untracked files fails unless forced' '
+	git reset --hard &&
+	git submodule update --recursive &&
+	(cd submod/subsubmod &&
+		echo X >untracked
+	) &&
+	test_must_fail git rm submod &&
+	test -d submod &&
+	test -f submod/.git &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect.modified actual &&
+	git rm -f submod &&
+	test ! -d submod &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	test_cmp expect actual
+'
+
+test_expect_success 'rm of a populated nested submodule with a nested .git directory fails even when forced' '
+	git reset --hard &&
+	git submodule update --recursive &&
+	(cd submod/subsubmod &&
+		rm .git &&
+		cp -a ../../.git/modules/sub/modules/sub .git &&
+		GIT_WORK_TREE=. git config --unset core.worktree
+	) &&
+	test_must_fail git rm submod &&
+	test -d submod &&
+	test -d submod/subsubmod/.git &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	! test -s actual &&
+	test_must_fail git rm -f submod &&
+	test -d submod &&
+	test -d submod/subsubmod/.git &&
+	git status -s -uno --ignore-submodules=none > actual &&
+	! test -s actual &&
+	rm -rf submod
+'
+
 test_done