diff --git a/CHANGES b/CHANGES
index 6d043f802..bef23d24b 100644
--- a/CHANGES
+++ b/CHANGES
@@ -68,6 +68,7 @@ Features added
 * #6232: Enable CLI override of Makefile variables
 * #6212 autosummary: Add :confval:`autosummary_imported_members` to display
   imported members on autosummary
+* #6271: ``make clean`` is catastrophically broken if building into '.'
 
 Bugs fixed
 ----------
diff --git a/sphinx/cmd/make_mode.py b/sphinx/cmd/make_mode.py
index 82a88933d..e87aa02fc 100644
--- a/sphinx/cmd/make_mode.py
+++ b/sphinx/cmd/make_mode.py
@@ -72,11 +72,19 @@ class Make:
 
     def build_clean(self):
         # type: () -> int
+        srcdir = path.abspath(self.srcdir)
+        builddir = path.abspath(self.builddir)
         if not path.exists(self.builddir):
             return 0
         elif not path.isdir(self.builddir):
             print("Error: %r is not a directory!" % self.builddir)
             return 1
+        elif srcdir == builddir:
+            print("Error: %r is same as source directory!" % self.builddir)
+            return 1
+        elif path.commonpath([srcdir, builddir]) == builddir:
+            print("Error: %r directory contains source directory!" % self.builddir)
+            return 1
         print("Removing everything under %r..." % self.builddir)
         for item in os.listdir(self.builddir):
             rmtree(self.builddir_join(item))