The authors have developed a simple, nested polymerase chain reaction (PCR) assay for amplification of an outer surface protein A (OspA) gene fragment of Borrelia burgdorferi using rapid temperature cycling and ethidium bromide detection on agarose gels, and applied it to the diagnosis of Lyme disease in humans. With denaturing and annealing temperature spikes instead of holds, cycle times were less than 20 minutes for a 30-cycle amplification. Using this rapid cycle PCR technique, as few as 5 spirochetes per mL of phosphate buffered saline were detected. In addition, B burgdorferi DNA was detected from spirochetes that had been spiked into one of several types of human body fluids including serum, synovial fluid, and cerebrospinal fluid (CSF). A number of clinical samples, which had been tested for Lyme immunoglobulin M (IgM) and immunoglobulin G (IgG) antibody were also examined. In 29 serologic positive samples (14 IgG and IgM positive, 9 IgM alone and 6 IgG alone), B burgdorferi DNA was not detected. In contrast, nine serum samples and one synovial fluid from patients with definite clinical features of Lyme disease were found to be negative by EIA and Western blot analysis for IgG and IgM antibody, but contained B burgdorferi DNA, as detected by PCR. Polymerase chain reaction analysis of serum and synovial fluid may be of significant diagnostic value in Lyme disease, especially in the absence of a serologic response in early, partially treated and seronegative chronic disease. This is the first study to report an association between PCR positivity and the absence of a serologic response to Lyme borreliosis.