Genes encoding two surface-expressed antigens of Ehrlichia chaffeensis, the variable-length PCR target (VLPT) and the 120-kDa antigen, which contain variable numbers of tandem repeats, were characterized for E. chaffeensis from white-tailed deer (Odocoileus virginianus). Both genes from infected deer contained numbers of repeats similar to those reported in genes from humans and ticks, although a new variant of the 120-kDa antigen gene containing five repeat units and coinfection with multiple VLPT and 120-kDa antigen gene genetic types were detected. Sequence analysis of both genes revealed more nucleotide variation than previously reported for E. chaffeensis from infected humans or ticks. This is the most extensive study of E. chaffeensis VLPT and 120-kDa antigen gene genetic variation to date and is the first to examine genetic variation in E. chaffeensis from a nonhuman vertebrate host.