The polymerase chain reaction (PCR) was used to amplify specific DNA sequences from different clinical isolates of Borrelia burgdorferi and from cerebrospinal fluid (CSF) of two patients with Lyme disease of the central nervous system. The amplification products were separated by polyacrylamide gel electrophoresis and visualised by ethidium bromide staining. The definitive identification of amplified DNA as a part of the B. burgdorferi flagellin gene was achieved by hybridisation to a 40-base oligonucleotide probe complementary to a part of the spirochaetal gene but not to the primers. Attempts to cultivate borreliae from either patient were unsuccessful and one patient had no serological marker in serum or CSF to indicate borreliosis. Clinical symptoms of both patients regressed with antibiotic therapy. The PCR system is a powerful and rapid technique to amplify flagellin gene sequences from CSF of patients with neuroborreliosis. Only one-tenth of the time needed for cultivation was required from CSF sampling to diagnosis. Gene amplification might, for the first time, allow effective monitoring of therapy for patients with Lyme disease of the central nervous system.