Your description sounds like you might want to build up a hash in the first while loop, with keys being $origin_service. Then you could check in the second loop whether a $destination_service is found among the origin services... (exists $services{$destination_service}).

BTW, it seems to me you've got a few typos in your code (e.g. $dest_service vs. $destination_service) — I could be wrong though...   Anyway, using strictures might help with that.

Often the answer to "compare this list with that list" is to populate a hash from one list and then look it up using items from the second list.

If you provide two lists with maybe 5 items in each and show us how you want to compare items from each list we may be able to help more. Trim each item down to just enough to demonstrate the problem btw.

stop_reference | service_id |     distance     | route_number
----------------+------------+------------------+--------------
 8888888888     |          2 |  137.74251340817 | 2
 1010101010     |          3 | 77.3369252039412 | 3
[download]

$connectsql = qq{SELECT b.service_id, d.stop_a, d.stop_b FROM bus_stop
+s a, routes b, service c, topology d WHERE a.stop_reference = c.stop_
+reference AND c.service_id = b.service_id AND a.stop_reference = d.st
+op_a ORDER BY a.stop_reference};
$sth = $dbh->prepare( $connectsql );
$sth->execute();
$sth->bind_columns( undef, \$connect_service, \$connect_stop, \$servic
+e_stop );
while( $sth->fetch() ) 
{
print.....
}

service_id |   stop_a   |   stop_b
------------+------------+------------
          3 | 1010101010 | 8888888888
          1 | 3333333333 | 6666666666
          2 | 6666666666 | 3333333333
          2 | 8888888888 | 1010101010
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Many others have suggested hashes, and that's definitely a valid approach. I'm curious, though, whether you couldn't achieve the same thing in SQL. That is, maybe you should just create a single query JOINing the two queries on service_id. That might reduce the amount of data you need to pull into Perl, and let the SQL server do the heavy lifting for you (which is what it's good at, after all).

Please try the SQL given below. This SQL is NOT tested, but should return records with origin_service == destination_service. Please refer to Subqueries with ANY, IN, and SOME

SELECT 
    a.stop_reference, 
    b.service_id, 
    distance(PointFromText('POINT($origin)', 27700),east_north), 
    c.route_number 
FROM 
    bus_stops a, 
    service b, 
    routes c 
WHERE 
    distance(PointFromText('POINT($origin)', 27700),east_north) < 200 
    AND 
        a.stop_reference = b.stop_reference 
    AND 
        b.service_id = c.service_id 
    AND
        b.service_id IN (
        SELECT 
            DISTINCT e.service_id 
        FROM 
            bus_stops d, 
            service e, 
            routes f 
        WHERE 
            distance(PointFromText('POINT($dest)', 27700),east_north) 
+< 200 
            AND 
            d.stop_reference = e.stop_reference 
            AND 
            e.service_id = f.service_id 
        ORDER BY 
            e.service_id, 
            distance(PointFromText('POINT($dest)', 27700),east_north) 
    )
ORDER BY 
    b.service_id, 
    distance(PointFromText('POINT($origin)', 27700),east_north)
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--VC

You need just one hash. Something like this

my %ids;

my @orig_service_ids = (3,1,4,9,7,12);

# this represents your first while ($sth->fetch) loop
for my $id (@orig_service_ids) {
    $ids{$id} = 1;
    # instead of '1', you could also assign something else as value,
    # e.g. an anonymous array [...], or an anonymous hash {...}, to
    # store associated data, which you could then retrieve later...
}

# ...

my @dest_service_ids = (1,5,8,11,7,2,9);

# this represents your second while ($sth->fetch) loop
for my $id (@dest_service_ids) {
    if (exists $ids{$id}) {
        print "ID $id exists in both origin and destination set\n";

        # ...
    }
}
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