Taenia solium has been ranked as the most important foodborne parasite and Taenia saginata as the most commonly found human Taenia tapeworm worldwide. The last official reports of taeniosis from Estonia were in 2003 for T. solium and 2012 for T. saginata. By law, all animal cases of cysticercosis must be registered and reported when found. Our aim was to estimate the prevalence of cysticercosis in Estonia caused by T. solium in pigs and T. saginata in cattle. The four slaughterhouses participating in the study slaughter between them approximately 80% of pigs and cattle in Estonia annually. Sampling spanned from February to April 2014, visiting the slaughterhouses five times per week. Visual inspection, palpation, and incisions at predilection sites were used to find cysts in both species. The sites inspected in both species were the external masseter, tongue, heart, and diaphragm. In addition, the internal masseter in pigs was examined, and the internal pterygoid muscle and esophagus in cattle. DNA was extracted from the cysts and used for PCR amplification of the cox1-gene for Taenia genus and species identification. A total of 564 cattle and 1217 pigs were examined. Cysts were found in 0.36% (n = 2; CI 0.06–1.17) of cattle and in 0.08% (n = 1; CI 0.004–0.40) of pigs. Cestode PCR was negative from all cysts. Results should be considered taking into account the low sensitivity and specificity of finding cysts. Results reflect the situation in larger slaughterhouses, and the possibility that the situation in smaller slaughterhouses is different should not be excluded.