Although Lyme disease is commonly seen in the southcentral United States, the epidemiology of the disease is poorly defined there. The purpose of this study was to document the presence of Borrelia burgdorferi in ticks collected in southeastern Missouri and around the city of St. Louis. Spirochetes were detected and identified as B. burgdorferi by immunofluorescent antibody (IFA) tests using the monoclonal antibody H5332 in 1.9% of Amblyomma americanum and 2.0% of Dermacentor variabilis ticks collected. The identity of IFA-positive organisms was verified by polymerase chain reactions (PCRs) with two different sets of B. burgdorferi-specific primers followed by Southern blotting. The DNA sequences of amplified 371-basepair PCR products from two positive Missouri ticks showed 97-98% identity with that obtained by the same method for the B31 strain of B. burgdorferi. These results confirm that B. burgdorferi is present in questing D. variabilis and A. americanum ticks in areas of Missouri where Lyme disease occurs. Additional studies are needed to determine the role of these ticks in the epidemiology of Lyme disease in Missouri and neighboring states.