Look at Sys::SigAction. From the POD:

          #timeout a system call:
          use Sys::SigAction qw( set_sig_handler );
          eval {
             my $h = set_sig_handler( 'ALRM' ,\&mysubname ,{ mask=>'AL
+RM' ,safe=>1 } );
             alarm(2)
             ... do something you want to timeout
             alarm(0);
          }; #signal handler is reset when $h goes out of scope
          alarm(0);
          if ( $@ ) ...
[download]

Sys::SigAction gives you the most reliable signal handling, and therefore timeout handling.