The aim of this research was to evaluate the effectiveness of excision versus swabbing as methods for the assessment of bovine and ovine carcass hygiene. Microbiological evaluation of bovine and ovine carcasses was performed by obtaining total viable counts (TVCs) and total Enterobacteriaceae counts (TECs) using excision and a swab (polyurethane) sampling method. Four anatomical locations were sampled on 30 bovine and 30 ovine carcasses, processed in four small (<10 animals per week) abattoirs. Excision and swab TVC were statistically similar (P<0.05) at all sites. The corresponding TECs were also statistically the same (P<0.05). Swabbing with the polyurethane sponge was therefore as effective as excision sampling for the determination of TVCs and TECs on bovine and ovine carcasses and may be used instead of excision sampling when assessing bovine and ovine carcass hygiene as per 2001/471/EC.