Microbiological results, obtained only at the end of the slaughtering process, do not provide information on the cause of the problem. Therefore, ‘process-based’ microbiological criteria which are based on values measured at various stages of the process, including final carcass values, should be used. Finally, in order to implement an adequate monitoring system, non-destructive techniques of carcass sampling could be used instead of excision. The microbial recovery may be lower, but it is proportional to the excision recovery and therefore, non-destructive techniques, like swabbing with sponges, could be a practical sampling method for the estimation of indicators during the slaughtering procedure and hygiene evaluation.