In spite of significant advances in immunologically based testing, accurate diagnosis of Lyme borreliosis remains problematic. To address this issue, a DNA amplification-based diagnostic test was developed utilizing the polymerase chain reaction (PCR) and oligonucleotide primers specific for the OspA and OspB genes of Borrelia burgdorferi. In this approach, a relatively large DNA fragment is amplified with an outer set of primers, and a "nested" internal sequence of the PCR product subsequently reamplified with an inner set of primers. This nested approach coupled with simple differential centrifugation allowed specific detection of as few as four B. burgdorferi organisms mixed in 2 ml of blood. This methodology was utilized on patients' samples, and it allowed detection of B. burgdorferi in the peripheral blood and urine of several individuals with clinical evidence of Lyme borreliosis. PCR became negative and symptoms improved following antibiotic therapy of treated individuals. These studies suggest that direct detection of Borrelia in infected individuals can aid in diagnosis and evaluation of therapy for Lyme borreliosis.