Tissues of rodents and host-seeking adult ticks collected in the Piedmont, Sandhills, Coastal Plain, and Coastal Zone of South Carolina were cultured in attempts to isolate Borrelia burgdorferi (Johnson, Schmid, Hyde, Steigerwalt & Brenner), the etiologic agent of Lyme disease. An exploratory, tree-based statistical analysis was used to identify ecological variables that were associated with spirochete infection among rodents and ticks. Spirochetes were isolated from tissues of 71 rodents: 22 (69%) of 32 eastern woodrats, 39 (53%) of 74 cotton mice, and 11 (25%) of 44 hispid cotton rats. Rodent infection prevalences were significantly higher in the Coastal Zone than in other regions. Spirochetes were also cultured from 31 (2.6%) of 1,193 questing ticks. Prevalence of spirochetes in Ixodes affinis Neumann (19/74, 26%) was significantly higher than in I. scapularis Say (12/864, 1.3%) and other species (0/255) of ticks tested. In addition, two (9%) of 23 adult I. minor Neumann removed from woodrats contained spirochetes. Isolates from rodents and ticks were analyzed immunologically by indirect immunofluorescence and Western blots, and further characterized by polymerase chain reaction assays and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. All were determined to be B. burgdorferi sensu lato. Results of this study confirmed that B. burgdorferi is endemic in South Carolina, and that enzootic transmission cycles exist at foci in the Coastal Zone. These findings add additional evidence that I. affinis and I. minor are potentially significant maintenance vectors of the spirochete.