Borrelia burgdorferi is the etiological agent of Lyme disease. Certain diagnostic problems associated with Lyme disease could be solved if a sensitive detection method were available for the pathogen: the polymerase chain reaction for the sensitive detection of Borrelia burgdorferi is a possible candidate. The latest methods for the amplification of Borrelia burgdorferi DNA are discussed. In particular, a method for the amplification of a Borrelia burgdorferi flagellin (41 kDa antigen) gene segment by the polymerase chain reaction is presented. Owing to its high degree of conservation between different Borrelia burgdorferi isolates, the flagellin gene is a suitable target sequence for gene amplification. In conclusion, the polymerase chain reaction is now ready to be used on clinical specimens. This technique will allow investigation of aspects concerning latency and recurrency of Borrelia burgdorferi in infected individuals.