Borrelia burgdorferi, the agent of Lyme disease, selectively expresses genes in the arthropod vector and mammalian host. Specific B. burgdorferi gene expression during human infection was examined in tissue specimens, using RNA-polymerase chain reaction, from 3 patients with Lyme disease. ospA was investigated because OspA is down-regulated by B. burgdorferi in ticks during engorgement and is a vaccine candidate in phase III clinical trials. p35 and p37 were also assessed because these genes are induced by spirochetes during murine Lyme borreliosis and play roles in protective immunity. p35 and p37 mRNA were detected in erythema migrans biopsy specimens from 2 patients and in the synovium of 1 patient with Lyme arthritis. ospA mRNA was not identified in any of these tissues. These data show that ospA is repressed while p35 and p37 are induced in human infection; these results are the first direct demonstration of differential B. burgdorferi gene expression during Lyme disease.