Index: cfe/trunk/lib/Format/TokenAnnotator.cpp
===================================================================
--- cfe/trunk/lib/Format/TokenAnnotator.cpp
+++ cfe/trunk/lib/Format/TokenAnnotator.cpp
@@ -1725,15 +1725,18 @@
       }
     }
 
-    if (NextNonCommentLine && CommentLine) {
-      // If the comment is currently aligned with the line immediately following
-      // it, that's probably intentional and we should keep it.
-      bool AlignedWithNextLine =
-          NextNonCommentLine->First->NewlinesBefore <= 1 &&
-          NextNonCommentLine->First->OriginalColumn ==
-              (*I)->First->OriginalColumn;
-      if (AlignedWithNextLine)
-        (*I)->Level = NextNonCommentLine->Level;
+    // If the comment is currently aligned with the line immediately following
+    // it, that's probably intentional and we should keep it.
+    if (NextNonCommentLine && CommentLine &&
+        NextNonCommentLine->First->NewlinesBefore <= 1 &&
+        NextNonCommentLine->First->OriginalColumn ==
+            (*I)->First->OriginalColumn) {
+      // Align comments for preprocessor lines with the # in column 0.
+      // Otherwise, align with the next line.
+      (*I)->Level = (NextNonCommentLine->Type == LT_PreprocessorDirective ||
+                     NextNonCommentLine->Type == LT_ImportStatement)
+                        ? 0
+                        : NextNonCommentLine->Level;
     } else {
       NextNonCommentLine = (*I)->First->isNot(tok::r_brace) ? (*I) : nullptr;
     }
Index: cfe/trunk/unittests/Format/FormatTest.cpp
===================================================================
--- cfe/trunk/unittests/Format/FormatTest.cpp
+++ cfe/trunk/unittests/Format/FormatTest.cpp
@@ -2595,21 +2595,85 @@
                    "code();\n"
                    "#endif",
                    Style));
-  // FIXME: The comment indent corrector in TokenAnnotator gets thrown off by
-  // preprocessor indentation.
-  EXPECT_EQ("#if 1\n"
-            "  // comment\n"
-            "#  define A 0\n"
-            "// comment\n"
-            "#  define B 0\n"
-            "#endif",
-            format("#if 1\n"
-                   "// comment\n"
-                   "#  define A 0\n"
-                   "   // comment\n"
-                   "#  define B 0\n"
-                   "#endif",
-                   Style));
+  // Keep comments aligned with #, otherwise indent comments normally. These
+  // tests cannot use verifyFormat because messUp manipulates leading
+  // whitespace.
+  {
+    const char *Expected = ""
+                           "void f() {\n"
+                           "#if 1\n"
+                           "// Preprocessor aligned.\n"
+                           "#  define A 0\n"
+                           "  // Code. Separated by blank line.\n"
+                           "\n"
+                           "#  define B 0\n"
+                           "  // Code. Not aligned with #\n"
+                           "#  define C 0\n"
+                           "#endif";
+    const char *ToFormat = ""
+                           "void f() {\n"
+                           "#if 1\n"
+                           "// Preprocessor aligned.\n"
+                           "#  define A 0\n"
+                           "// Code. Separated by blank line.\n"
+                           "\n"
+                           "#  define B 0\n"
+                           "   // Code. Not aligned with #\n"
+                           "#  define C 0\n"
+                           "#endif";
+    EXPECT_EQ(Expected, format(ToFormat, Style));
+    EXPECT_EQ(Expected, format(Expected, Style));
+  }
+  // Keep block quotes aligned.
+  {
+    const char *Expected = ""
+                           "void f() {\n"
+                           "#if 1\n"
+                           "/* Preprocessor aligned. */\n"
+                           "#  define A 0\n"
+                           "  /* Code. Separated by blank line. */\n"
+                           "\n"
+                           "#  define B 0\n"
+                           "  /* Code. Not aligned with # */\n"
+                           "#  define C 0\n"
+                           "#endif";
+    const char *ToFormat = ""
+                           "void f() {\n"
+                           "#if 1\n"
+                           "/* Preprocessor aligned. */\n"
+                           "#  define A 0\n"
+                           "/* Code. Separated by blank line. */\n"
+                           "\n"
+                           "#  define B 0\n"
+                           "   /* Code. Not aligned with # */\n"
+                           "#  define C 0\n"
+                           "#endif";
+    EXPECT_EQ(Expected, format(ToFormat, Style));
+    EXPECT_EQ(Expected, format(Expected, Style));
+  }
+  // Keep comments aligned with un-indented directives.
+  {
+    const char *Expected = ""
+                           "void f() {\n"
+                           "// Preprocessor aligned.\n"
+                           "#define A 0\n"
+                           "  // Code. Separated by blank line.\n"
+                           "\n"
+                           "#define B 0\n"
+                           "  // Code. Not aligned with #\n"
+                           "#define C 0\n";
+    const char *ToFormat = ""
+                           "void f() {\n"
+                           "// Preprocessor aligned.\n"
+                           "#define A 0\n"
+                           "// Code. Separated by blank line.\n"
+                           "\n"
+                           "#define B 0\n"
+                           "   // Code. Not aligned with #\n"
+                           "#define C 0\n";
+    EXPECT_EQ(Expected, format(ToFormat, Style));
+    EXPECT_EQ(Expected, format(Expected, Style));
+  }
   // Test with tabs.
   Style.UseTab = FormatStyle::UT_Always;
   Style.IndentWidth = 8;