Index: lib/Support/FileCheck.cpp
===================================================================
--- lib/Support/FileCheck.cpp
+++ lib/Support/FileCheck.cpp
@@ -737,6 +737,8 @@
   // LineNumber keeps track of the line on which CheckPrefix instances are
   // found.
   unsigned LineNumber = 1;
+  bool HasNonLabelPrefix = false;
+  StringRef MatchedPrefix;
 
   while (1) {
     Check::FileCheckType CheckTy;
@@ -746,6 +748,7 @@
                                                    CheckTy);
     if (UsedPrefix.empty())
       break;
+    MatchedPrefix = UsedPrefix;
     assert(UsedPrefix.data() == Buffer.data() &&
            "Failed to move Buffer's start forward, or pointed prefix outside "
            "of the buffer!");
@@ -763,8 +766,11 @@
       return true;
     }
 
-    // Okay, we found the prefix, yay. Remember the rest of the line, but ignore
-    // leading whitespace.
+    // Okay, we found the prefix, yay.
+    if (CheckTy != Check::CheckLabel)
+      HasNonLabelPrefix = true;
+
+    // Remember the rest of the line, but ignore leading whitespace.
     if (!(Req.NoCanonicalizeWhiteSpace && Req.MatchFullLines))
       Buffer = Buffer.substr(Buffer.find_first_not_of(" \t"));
 
@@ -840,6 +846,12 @@
     return true;
   }
 
+  if (!HasNonLabelPrefix)
+    SM.PrintMessage(SMLoc::getFromPointer(Buffer.data()),
+                    SourceMgr::DK_Warning,
+                    "Prefix " + MatchedPrefix + " only occurs in a LABEL check, "
+                    "this is probably not what you want.");
+
   return false;
 }
 
Index: test/FileCheck/check-prefixes-only-labels.txt
===================================================================
--- /dev/null
+++ test/FileCheck/check-prefixes-only-labels.txt
@@ -0,0 +1,6 @@
+// RUN: FileCheck -check-prefix=FOO -input-file %s %s 2>&1 | FileCheck -check-prefix=WARNING %s
+
+foo
+; FOO-LABEL: foo
+
+; WARNING: warning: Prefix FOO only occurs in a LABEL check, this is probably not what you want.
Index: test/FileCheck/check-prefixes-only-labels2.txt
===================================================================
--- /dev/null
+++ test/FileCheck/check-prefixes-only-labels2.txt
@@ -0,0 +1,13 @@
+// RUN: FileCheck -vv -check-prefixes=FOO,BAR -input-file %s %s 2>&1 | FileCheck -check-prefix=DONTWARN %s
+
+; Prefix FOO is only checked as a label check, but BAR is checked, that's why we
+; shouldn't produce a diagnostic that there is a prefix only used in label checks:
+;
+; DONTWARN-NOT: warning: Prefix {{.*}} only occurs in a LABEL check, this is probably not what you want.
+
+foo
+; FOO-LABEL: foo
+
+bar
+; BAR: bar
+
Index: test/FileCheck/check-prefixes-only-labels3.txt
===================================================================
--- /dev/null
+++ test/FileCheck/check-prefixes-only-labels3.txt
@@ -0,0 +1,11 @@
+// RUN: FileCheck -vv -check-prefix=FOO -input-file %s %s 2>&1 | FileCheck -check-prefix=DONTWARN %s
+
+; This is a very normal test, so make sure we don't complain about it:
+;
+; DONTWARN-NOT: warning: Prefix FOO only occurs in a LABEL check, this is probably not what you want.
+foo
+bar
+
+; FOO-LABEL: foo
+; FOO:       bar
+