Tonsils of 457 fattening pigs from Estonia (n = 151), Latvia (n = 109), and the Leningrad Region of Russia (n = 197) were collected between 2004 and 2007 to study the prevalence of enteropathogenic Yersinia in slaughter pigs. Yersinia enterocolitica and Yersinia pseudotuberculosis were isolated by selective and cold enrichment. Pathogenic Y. enterocolitica and Y. pseudotuberculosis were identified by PCR targeting the chromosomal genes ail and inv, respectively. The presence of the virulence plasmid was confirmed by PCR targeting the virF gene of Y. enterocolitica and Y. pseudotuberculosis. The prevalence of ail-positive Y. enterocolitica was 89% in Estonia, 64% in Latvia, and 34% in Russia, with 81% of ail-positive samples being virF-positive. A statistically significant (p < 0.05) difference between Estonian and Latvian pigs and between pigs from Latvia and the Leningrad Region of Russia was observed when assuming randomized sampling. Y. enterocolitica bioserotype 4/O:3 was the only pathogenic type found. The prevalence of inv and virF-positive Y. pseudotuberculosis was higher in Russia (7%) than in Latvia (5%) and Estonia (1%), with a statistically significant difference between pigs from Estonia and the Leningrad Region of Russia when assuming both randomized sampling and clustering at farms. All Y. pseudotuberculosis isolates were bioserotype 2/O:3. A total of eight pigs (2%), one pig from Latvia and seven pigs from the Leningrad Region of Russia, carried both pathogenic Y. enterocolitica and Y. pseudotuberculosis in the tonsils. Cold enrichment was found to be a more efficient method compared to selective enrichment to isolate both species. Pigs seem to be an important reservoir of human enteropathogenic Y. enterocolitica 4/O:3 and Y. pseudotuberculosis 2/O:3 in these countries.