The prevalence of human pathogenic Yersinia enterocolitica isolates in livestock farming is of paramount interest. Raw goat milk has been proposed as a source of human yersiniosis; however, no data on the prevalence of human strains of Y. enterocolitica in goat herds are available. Therefore, fecal samples (n = 575) were collected from 24 goat herds from Lower Saxony, northern Germany. Pre-enrichment in peptone, sorbitol and bile salts broth was followed by plating on cefsuloidin irgasan novobiocin agar. Yersinia enterocolitica was isolated from 17 (3%) samples of five (21%) goat herds. All isolates were biovar 1A, but represented various serovars. PCR assays targeting Yersinia adhesin (yad) gene and the yopT gene, both associated with pathogenicity, produced no amplification products. Therefore, the isolates can be regarded as opportunistic apathogenic bacteria. Consequently, milk, cheese or meat from goats should not be considered as an important source for human yersiniosis.