diff --git a/cachegrind/cg_annotate.in b/cachegrind/cg_annotate.in
index bcb98935b..1daa15da2 100644
--- a/cachegrind/cg_annotate.in
+++ b/cachegrind/cg_annotate.in
@@ -398,7 +398,9 @@ sub read_input_file()
 
     # Read body of input file.
     while (<INPUTFILE>) {
-        s/#.*$//;   # remove comments
+        # Skip comments and empty lines.
+        next if /^\s*$/ || /^\#/;
+
         if (s/^(-?\d+)\s+//) {
             my $lineNum = $1;
             my $CC = line_to_CC($_);
@@ -436,9 +438,6 @@ sub read_input_file()
             # Assume that a "fn=" line is followed by a "fl=" line.
             $currFileFuncName = undef;
 
-        } elsif (s/^\s*$//) {
-            # blank, do nothing
-        
         } elsif (s/^summary:\s+//) {
             $summary_CC = line_to_CC($_);
             (scalar(@$summary_CC) == @events) 
diff --git a/callgrind/callgrind_annotate.in b/callgrind/callgrind_annotate.in
index e18ed4ed9..8854aee13 100644
--- a/callgrind/callgrind_annotate.in
+++ b/callgrind/callgrind_annotate.in
@@ -420,10 +420,8 @@ sub read_input_file()
     # Read header
     while(<INPUTFILE>) {
 
-      # remove comments
-      s/#.*$//;
-
-      if (/^$/) { ; }
+      # Skip comments and empty lines.
+      if (/^\s*$/ || /^\#/) { ; }
 
       elsif (/^version:\s*(\d+)/) {
 	# Can't read format with major version > 1
@@ -540,9 +538,11 @@ sub read_input_file()
 
     # Read body of input file.
     while (<INPUTFILE>) {
+        # Skip comments and empty lines.
+        next if /^\s*$/ || /^\#/;
+
 	$prev_line_num = $curr_line_num;
 
-        s/#.*$//;   # remove comments
         s/^\+(\d+)/$prev_line_num+$1/e;
         s/^\-(\d+)/$prev_line_num-$1/e;
         s/^\*/$prev_line_num/e;
@@ -646,9 +646,6 @@ sub read_input_file()
             $curr_fn_CC = $fn_totals{$curr_name};
             $curr_fn_CC = [] unless (defined $curr_fn_CC);
 
-        } elsif (s/^\s*$//) {
-            # blank, do nothing
-
         } elsif (s/^cob=(.*)$//) {
 	  $curr_cobj = uncompressed_name("ob",$1);