The paper analyses the results of serological examinations of domestic, farm and free-living animals from different regions of Slovakia, Southern Moravia, Southern Bohemia and Southern Poland using ELISA, indirect hemagglutination assay (IHA) and Western blot (WB). In Slovakia, significantly higher seroprevalence was recorded in dogs (33.5%) than in horses (26.5%), cattle (22.5%), sheep (16.6%) and rodents (17.8%) by using a mixture of Borrelia garinii, B. afzelii, B. burgdorferi sensu stricto (s.s.) antigens in ELISA. Seroprevalence in horses was significantly higher than in sheep and rodents, and seroprevalence in cattle was significantly higher than in rodents. By using IHA in free-living species, the highest seropositivity rates were detected in fallow deer (40.7%) compared with moufflons (16.6%), pheasants (8.0%) and pigeons (1.2%). When testing sera of horses, dogs and cattle from Slovakia by using different Slovak B. burgdorferi sensu lato (s.l.) isolates as antigens in ELISA, significantly higher seroprevalence of anti-Borrelia IgG antibodies and consistency of positive and negative findings was detected in comparison when American isolates were used. In WB analyses using the Eurocarpathian antigens, dog sera from Eastern Slovakia and Southern Moravia showed statistically insignificant differences in sensitivity and consistency of positive and negative findings. By using different methods and antigens in the same group of dog sera, significant differences in seroprevalence were only found in IHA with a mixture of Euroamerican B.b.s.l and WB CB26 B.b.s.s. In addition to other factors, the complexity of the standardization of the assay system with regard to the genetic and geographical heterogeneity of B. burgdorferi s.l. isolates used as antigens is also discussed.