In the course of epizootological research on Lyme borreliosis in animals, the serological evidence of this zoonosis in horses and cattle from different voivodships of Poland was screened. We also discussed some diagnostic problems of Lyme borreliosis resulting from, in addition to other factors, genetic and geographical heterogeneity isolates B. burgdorferi s.l. used as antigens. Using ELISA from 395 sera of horses the total mean seroprevalence for anti-Borrelia IgG antibodies 25.6% was observed. In the respective years, significant differences in the mean seroprevalence were not recorded. In the voivodships, the total mean seroprevalence and mean seroprevalence for the respective years varied from 16.6–66.6%. An analysis of seroprevalence depending on the age showed a significant difference between 0–2 year-old horses compared to older horses. The total seroprevalence in the set of 98 serum samples was lower with the strain of B. garinii (25.5%) compared to a mixture of B. burgdorferi sensu stricto with B. afzelii (36.7%) and B. afzelii (42.8%). The highest correlation of fi ndings was reached comparing the strains of B. afzelii (South Poland) and a mixture of B. burgdorferi s. s. + B. afzelii (East Slovakia). Lower correlation was between B. garinii and mixture of B. burgdorferi s. s. + B. afzelii. On the contrary, the lowest correlation of findings was observed between the Slovak strain of B. garinii and Polish B. afzelii. In a group of 26 cow sera, the mean seroprevalence for anti-Borrelia IgG antibodies was 26.9%. In the remaining clinical signs the seroprevalence was 28.5–66.6%. In Western blot, out of 25 examined sera of horses 15 (60.0%) were positive, out of 6 cows 5 (83.3%) were positive (2 lameness, 2 phlebitis, 1 clinically healthy). The horses and cows sera recognised the proteins: 93 (MEP)-, 83-, 75-, 66-, 55-, 43-, 45-, 41 (flagellin)-, 39-, 34-, 35 (OspB) and 25-, 28 (OspC)-kDa. These results alert veterinarians to take into account the aetiology of Lyme disease in differential diagnoses.