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The recent proposals for modernization of the meat inspection system across the EU recommend that it should be risk-based and also suggest that risk categorization of slaughterhouses should be based on a process hygiene output through the use of indicator organisms – Aerobic Colony Count (ACC) and Enterobacteriaceae count (EC), monitored on carcasses. In this study, the evaluation of the hygiene of operations in cattle and pig slaughterhouses/meat processing companies in Serbia was carried out through two methodologies: a) auditing based on scoring systems used in the UK and Australia; and b) microbial process hygiene indicators. The results confirmed that slaughterhouses with higher levels of hygiene had lower ACC and EC levels. The complementary nature of the methodologies may be effectively used in a process of risk categorization of slaughterhouses. To achieve better consistency and objectiveness in the assessment process, the intensive and structured training of regulatory authorities (official veterinary inspectors, meat inspectors) will be essential. [ABSTRACT FROM AUTHOR]