Bovine cysticercosis and hydatidosis are frequently identified by inspectors in slaughterhouses from the state of Rio Grande do Sul. Slaughterhouse records can provide valuable information for animal-related diseases and public health surveillance. Analyzing these data can aid set priorities to regions or properties that need more attention. Slaughter condemnation data is collected daily and stored in the Agricultural Defense System (SDA) database of the State Veterinary Services. However, it needs to be turned into useful information in bovine cysticercosis and hydatidosis surveillance programs. This study aimed to discuss how the analysis of condemnation data in the context of epidemiology can be useful for a surveillance system of bovine cysticercosis and hydatidosis. For this purpose, slaughter data of 5,137,870 cattle from 480,000 animal movement permits (GTA) from 97,891 farms from 2014 to 2018 were obtained from the Secretary of Agriculture, Livestock and Rural Development of the State of Rio Grande do Sul (SEAPDR-RS). Differences in the occurrence rates of bovine cysticercosis and hydatidosis among mesoregions over time were assessed through generalized linear models. Cysticercosis was identified in 65,379 (1.27%) carcasses and hydatidosis in 323,395 (6.29%). The occurrence rates of both diseases varied distinctly over time between the regions (p<0.01). Next, a process was developed to identify priority farms to target a surveillance program based on the prevalence. Period prevalence for cysticercosis and hydatidosis was obtained for each farm. The epidemiological indicator was calculated for each farm, dividing the number of affected carcasses by the number of bovines sent to slaughter during the period. The mean prevalence was obtained, and the exact binomial test was applied to identify farms presenting prevalence above the mean. It was observed that 2.48% and 6.17% of the farms had prevalence above the population mean prevalence of cysticercosis and hydatidosis, respectively. The Western mesoregion had the highest percentage of farms with prevalence above the average for cysticercosis (6.9%), followed by the Southwest mesoregion (6.0%). For hydatidosis, the percentage frequency of farms with prevalence above the average was markedly higher in the mesoregions Southeast (32.8%) and Southwest (29.5%). The results showed that analysis of slaughterhouse condemnation data of SDA is useful to identify situations in which the occurrence of the diseases is significantly higher than the average to apply additional measures or epidemiological investigations. This information may be useful in plans of epidemiological surveillance programs for controlling bovine cysticercosis and hydatidosis by the State’s Official Veterinary Services.