To evaluate the effectiveness of bagging of the rectum in mitigating the contamination of carcasses with enteropathogenic Yersinia at the slaughterhouse and to estimate the hidden prevalences of these pathogens in different farm types and capacities, samples from pigs, carcasses, and slaughterhouse environment were collected, and a Bayesian probability model was constructed. In addition, the contamination routes were studied with molecular typing of the isolated strains. According to the model, bagging of the rectum reduced carcass contamination significantly with pathogenic Yersinia enterocolitica, but not with Yersinia pseudotuberculosis, and alone it was insufficient to completely prevent the carcass contamination with enteropathogenic Yersinia. The hidden prevalence of pathogenic Y. enterocolitica was higher at high production capacity than it was in low production capacity, but the 95 % credible intervals overlapped. Slaughterhouse environments can contaminate carcasses with enteropathogenic Yersinia, but the plausible main contamination source is the pig carrying the pathogen.