I had a similar problem and was able to solve it by disabling AutoCommit       my $dbh = DBI->connect("DBI:mysql:database=$database;host=localhost", ,$uname, $pswd,  {'RaiseError' => 1, AutoCommit => 0}); and then only committing changes after I had executed many-many execute statements...

my $max_rows_commit = 0;
my $store = $dbh->prepare('INSERT ... ');
foreach my $row (@rows){
    $store->execute($row);
    $max_rows_commit++;
    if ($max_rows_commit >10000){
        $dbh->commit;
        $max_rows_commit = 0;
    }
}
$dbh->commit;
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A better reference for how to speed up DBI commands can be found here: http://www.perlmonks.org/bare/?node_id=273952 Good luck!