The genes coding for the outer surface protein (OspA) of Borrelia burgdorferi, the causative agent of Lyme borreliosis have been cloned and sequenced. Two German strains (skin isolate PKo and cerebrospinal fluid isolate PBi) have been analyzed. Using an OspA-specific monoclonal antibody (L32 2E7) for immunological screening of a genomic pUC18 library of B. burgdorferi strain PKo, and OspA-producing clone was detected and subclones containing the open reading frame were constructed. The gene coding for the OspA protein of B. burgdorferi strain PBi was amplified using polymerase chain reaction (PCR) and cloned in pUC8. The open reading frame of both ospA genes consists of 822 nucleotides corresponding to a protein of 273 amino acids. Both proteins have a calculated molecular mass of 29.6 kDa. Molecular analysis revealed significant differences between each other and to already-published sequences of ospA of B. burgdorferi strains B31, ZS7 and N40 (the ospA genes of B31, ZS7 and N40 are nearly identical). The deduced amino acid sequences of the OspA protein of strains PKo and PBi showed a homology of 83% to each other and 77% and 80%, respectively, to OspA protein of strain B31. The three proteins contain a variable middle region, whereas the N and the C terminus are conserved. This unexpected high dissimilarity of the ospA genes may be important in respect to vaccination studies and diagnostic procedures (i.e., development of PCR primers or serodiagnostic antigens). Moreover, the molecular heterogeneity of OspA confirms three out of seven immunologically defined OspA serotypes of a recently proposed OspA serotyping system.