I just test the code above, and it does indeed work.

Out of curiosity I benchmarked the two solutions, and merlyn's is twice as fast! (nice).

However, I would consider mine easier to follow, but maybe that is just because I wrote it. I think I will have to look into using subsrting and pos for performance issues though.
Here is my test code: 
#!/usr/bin/perl
use Benchmark;

#get start and end comment
my $start = $ARGV[0];
my $end   = $ARGV[1] || "\n";

my $file;
open(FILE, "test.txt") || die;
{
    local $/ = undef; #set to 'slurp' mode
    $file = <FILE>;      #read entire file into $_
}
close FILE;

timethese(100000, {
    'parse1' => sub { &parse1($file) },
    'parse2' => sub { &parse2($file) },
});

sub parse1
{   my $file = shift;
    while( $file =~ /\Q$start\E(.*?)\Q$end\E/sg )
    {
        $a = $1;
        $match = $&;
 
        #look for more start tags in what we matched
        while( $a =~ /\Q$start\E/sg )
        {
            #balance the ending comments
            $file =~ /.*?\Q$end\E/sg;
            $match .= $&;
        }
        #print $match, "\n";
    }
    
    return $match;
}

sub parse2
{
    my $file = shift;
    my $inside = 0;
    my $oldpos = 0;
    while ($file =~ /(\Q$start\E|\Q$end\E)/g) {
      if ($1 eq $start) {
        if (++$inside == 1) {
          $oldpos = pos($file) - length($start);
        }
      } else {
        if (--$inside == 0) {
          return substr($file, $oldpos, pos($file)-$oldpos);
        }
      }
    }
}

[download]
And here is my results (I used the same test.txt as my post above): 
prompt% parse.pl '/*' '*/'
Benchmark: timing 100000 iterations of parse1, parse2...
    parse1: 42 wallclock secs (30.07 usr +  0.11 sys = 30.18 CPU)
    parse2: 17 wallclock secs (13.60 usr +  0.04 sys = 13.64 CPU)

[download]

In reply to Re: matching comments by perlmonkey
in thread matching comments by Eugene

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