The ospC gene coding for the outer surface protein OspC and the fla gene coding for the flagellin have been investigated in three different Borrelia burgdorferi sensu lato strains. These strains (the North American strain B31 and the European strains PKo and PBi) derive from various biological sources (lxodes dammini, human skin and human CSF) and belong to three different B. burgdorferi OspA serotypes and genospecies (OspA serotype 1, B. burgdorferi sensu stricto; OspA serotype 2, group VS461 and OspA serotype 4, B. garinii, respectively). The ospC and fla genes of the respective strains have been amplified by polymerase chain reaction, cloned in pUC8 and sequenced. The fla as well as the ospC genes were different among the three strains investigated. In general the fla genes are more conserved than the ospC genes. The fla genes have the same length of 1008 nucleotides coding for proteins of 336 amino acids, whereas the ospC genes differ in length. The ospC genes of strains B31, PKo and PBi have 630, 636 and 621 nucleotides encoding proteins of 210, 212 and 207 amino acids, respectively. The ospC genes exhibit sequence identities between 70% and 74% among each other, sequence identities of the fla genes are in the range 96-97%. The ospC genes could be expressed in Escherichia coli to obtain proteins with and without leader peptides. The expression of the fla gene and an internal gene fragment resulted in the complete flagellin protein and a truncated protein (amino acids 129-251). The different ospC and fla gene products were immunoreactive with monoclonal antibodies and human sera and, thus, enlarge the spectrum of recombinant antigens to improve antibody detection in patients with Lyme borreliosis.