use IO::Handle; my @logmessages; my $stderr = IO::Handle->new; $stderr->autoflush( 1 ); $stderr->fdopen( fileno( STDERR ), 'r' ); system( 'command', 'with', 'args' ); while( defined( my $line = $stderr->getline ) ) { push @logmessages, $line; } $stderr->close; # now do something useful with @logmessages