diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlHealthcheck.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlHealthcheck.pm
index 47cccb6983306e4f40a1fb69b76800aaddc463e3..079340eda0df863d9dd1ccde148294b1b67a9906 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlHealthcheck.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlHealthcheck.pm
@@ -136,6 +136,11 @@ sub _run_test {
     my $reference_size = $test->{reference_size};
     my $logical_test = $test->{logical_test};
 
+    # Final semicolons are removed if present
+    if ($query =~ /(;\s*$)/) {
+        $query =~ s/$1//;
+    }
+
     print "Test description: $description\n";
     print "Checking whether the number of rows $logical_test $reference_size\n";