To determine whether the polymerase chain reaction could contribute to a better diagnosis of Lyme disease, skin biopsy samples from patients suffering from erythema chronicum migrans or acrodermatitis chronica atrophicans were tested for the presence of Borrelia burgdorferi by a polymerase chain reaction assay, which was specific for European strains. The spirochete could not be detected microscopically in any of the 15 biopsy samples obtained from nine patients. However, B. burgdorferi could be isolated from seven of eight of these samples, which indicated the presence of spirochetes. Using a nested polymerase chain reaction, we were able to detect B. burgdorferi-specific sequences in 12 of the 15 biopsy samples. Biopsy samples from three of four patients with erythema chronicum migrans and four of five patients with acrodermatitis chronica atrophicans were found to be positive for B. burgdorferi. The spirochete could be isolated from the biopsy sample, from a patient with erythema chronicum migrans who tested negative, which suggests a false-negative polymerase chain reaction result probably on account of the low number of spirochetes present in the lesion. The positive polymerase chain reaction for lesions from patients with acrodermatis chronica atrophicans supports the concept that B. burgdorferi can persist in the skin over a long period of time. From these results, it was concluded that the polymerase chain reaction is a valuable technique for the diagnosis of Lyme disease.