Meat inspection data can provide valuable information about herd health to producers, veterinarians and veterinary authorities and can be used as a feedback system for farmers to improve their herd management. The aim of this study was to analyse the influence of agricultural holdings, slaughterhouses and time periods (quarters) on the occurrence and composition of the prevalence of post-mortem findings of 4 million pigs slaughtered in Austria in 2016, by applying a permutation multivariate analysis of variance. Pneumonia (21.9%) and milk spots (19.9%) were the most frequently recorded conditions. Our analysis indicated a statistically significant influence of all three considered factors (agricultural holdings, slaughterhouses and periods) on the prevalence of post-mortem findings. The observed prevalence could not only be explained by the differences between the farms of origin and slaughterhouses but also by the variability within the slaughterhouses. Much of the explained variance of the prevalence was due to differences between producers (mean R2 = 0.61), followed by slaughterhouses (mean R2 = 0.19) and period (mean R2 = 0.05). To meet the demand for a valid feedback system to farmers and attending veterinarians, a robust and ideally more detailed recording of frequent pathologies, especially those affecting the respiratory tract and the liver, should be developed.