Skin biopsy samples from 150 patients with typical cutaneous manifestation of Lyme borreliosis, erythema migrans, were cultivated for the presence of Borrelia burgdorferi sensu lato in modified Kelly Pettenkofer (MKP) medium and analysed with two different polymerase chain reactions using either flagellin or nested OspA primers. Cultivation was successful in 75 of 150 (50%) skin samples. Out of 70 strains that were typed using PFGE, B. afzelii was identified in 60 (86%), B. garinii in 10 (14%) specimens, while no B. burgdorferi sensu stricto strains were found. B. burgdorferi sensu lato DNA was detected with polymerase chain reaction in 28% and 61% of skin samples, using flagellin and nested OspA primers, respectively. Concordant results in all three procedures employed in the present study were found in 62 (41%) specimens: 25/150 (17%) were positive with all three methods and 37/150 (25%) samples were completely negative.