Heads of hunter-harvested deer and elk were collected throughout South Dakota (USA) and within established chronic wasting disease (CWD) surveillance areas from 1997–2002 to determine infection with CWD and bovine tuberculosis (TB). We used immunohistochemistry to detect CWD-infected individuals among 1,672 deer and elk sampled via geographically targeted surveillance. A total of 537 elk (Cervus elaphus nelsoni), 813 white-tailed deer (Odocoileus virginianus), and 322 mule deer (O. hemionus) was sampled for CWD. Estimated overall prevalence and associated confidence intervals (95%) in white-tailed deer was 0.001% (0–0.007%). Similarly, estimated overall prevalence in elk and mule deer was 0.0% (0–0.004%) and 0.0% (0–0.011%), respectively. A total of 401 elk, 1,638 white-tailed deer, and 207 mule deer was sampled for TB. Estimated overall prevalence of infection with TB in elk harvested in South Dakota was 0.0% (0–0.009%). Similarly, estimated overall prevalence of TB in white-tailed deer and mule deer harvested throughout South Dakota was 0.0% (0–0.002%) and 0.0% (0–0.018%), respectively.