diff --git a/llvm/utils/UpdateTestChecks/common.py b/llvm/utils/UpdateTestChecks/common.py
--- a/llvm/utils/UpdateTestChecks/common.py
+++ b/llvm/utils/UpdateTestChecks/common.py
@@ -479,6 +479,9 @@
   # prefix_exclusions are prefixes we cannot use to print the function because it doesn't exist in run lines that use these prefixes as well.
   prefix_exclusions = set()
   printed_prefixes = []
+  # A mapping of prefixes to the run lines they exist in.
+  prefix_to_lines = {}
+
   for p in prefix_list:
     checkprefixes = p[0]
     # If not all checkprefixes of this run line produced the function we cannot check for it as it does not
@@ -487,6 +490,11 @@
     if any(map(lambda checkprefix: func_name not in func_dict[checkprefix], checkprefixes)):
         prefix_exclusions |= set(checkprefixes)
         continue
+    for prefix in checkprefixes:
+        if prefix not in prefix_to_lines:
+            prefix_to_lines[prefix] = []
+        prefix_to_lines[prefix].append(p)
+
 
   # prefix_exclusions is constructed, we can now emit the output
   for p in prefix_list:
@@ -515,6 +523,9 @@
 
       vars_seen = set()
       printed_prefixes.append(checkprefix)
+      # For this function we can't use any of the other prefixes that exists in the run lines
+      # that this prefix is in.
+      prefix_exclusions |= { prefix for prefix in p[0] for p in prefix_to_lines[prefix] }
       attrs = str(func_dict[checkprefix][func_name].attrs)
       attrs = '' if attrs == 'None' else attrs
       if attrs: