This study investigated the prevalence of Yersinia enterocolitica (YE) bio/serotypes and YE-like species in clinical stool specimens. The special aim was to find the best methods for accurate identification of YE species and, further, pathogenic strains among YE isolates. Of the 41,848 specimens cultured in ten laboratories during a 12-month period, 473 Yersinia strains were isolated from 462 patients. The strains were identified by 21 biochemical tests, serotyping, colony morphology, as well as by 16S rRNA and gyrB gene sequencing. The most prevalent Yersinia findings were YE biotype 1A (64% of the strains) and pathogenic bio/serotype 4/O:3 (16%). The cold-enrichment increased the number of all isolates, and 25% of the bio/serotype 4/O:3 and 2/O:9 strains were only found by cold-enrichment. In routine diagnostic laboratories, 50% of the YE-like species were identified as YE and in 26% the identification differed from that of the reference laboratory. The microscopic colony identification on CIN agar with positive CR-MOX test, combined with several biochemical tests, identified reliably the pathogenic YE bioserotypes and most YE BT 1A strains, but some strains of the YE-like species were so heterogenic that gene sequencing was the only way to identify them.