Thank you very much! I am using the first suggestion, as I don't really understand the binary search yet, and so far it doesn't seem to have problems with searching the 500,000 rows.

I am now running into the problem of the results being output on different lines in the resulting CSV file for each print command. Here is my code:

#!/usr/bin/perl
use warnings;
use strict;

open my $GENES,     '<', 'chr1data.csv'     or die $!;
open my $LOCATIONS, '<', 'chr1snps.csv' or die $!;

chomp(my @locations = map { (split ',')[2] } <$LOCATIONS>);
# If IDs are not already sorted, uncomment the following line:
# @locations = sort { $a <=> $b } @locations;

for (<$GENES>) {
    my ($chromosome, $start, $end) = split ',';
    print "$chromosome,$start,$end";
    my $idx = 0;        # For $end, start searching where you left for
+ $start.
    my $correction = 0; # Needed for Start(-) == Start and End(+) == E
+nd.
    for my $pos ($start, $end) {
        $idx++ while $locations[$idx] <= $pos - $correction
                     and $idx <= $#locations;
        die "No numbers around $pos ($idx) \n"
            if $idx == 0 or $idx > $#locations;
        print ",$locations[$idx-1],$locations[$idx]";
        $correction = 1;
    }
    print "\n";
}
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Printing print ",$locations[$idx-1],$locations[$idx]"; puts this information on a new line. I'd like it to come out on the same line as print "$chromosome,$start,$end"; for each search. Do I have a \n in the wrong place?