Contagious equine metritis (CeM) is a highly contagious venereal disease caused by the bacterium Taylorella equigenitalis. In Croatia, horses are almost never tested for this disease unless it is specifically requested. to date, no positive bacteriology results for T. equigenitalis have ever been obtained in Croatia. During 2014 and 2015, 12 animals were screened for T. equigenitalis using both bacteriology and a polymerase chain reaction (PCr) test. No positive cultures were obtained, however, samples from three animals tested positive on PCr. Sequencing of the PCr products revealed that one animal was positive for T. equigenitalis and two animals for T. asinigenitalis. These results represent the first evidence of T. equigenitalis and T. asinigenitalis infections in horses in Croatia. the high prevalence of T. equigenitalis and T. asinigenitalis positive horses (n = 3) in the population tested (n = 12) strongly suggests that the overall prevalence of horses positive for Taylorella spp. in Croatia is high, and that the equine population, especially those animals used for breeding, should be regularly tested for this bacterium. In addition, these results show the low sensitivity of using culture alone and that additional molecular methods should be utilised to identify positive cases of Taylorella spp.