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Endemic foci of human African trypanosomiasis are present in southern Sudan. In 1996 and 1997, trypanosomiasis increased sharply in Tambura County. To define the magnitude and geographic distribution of the outbreak, we conducted a prevalence survey using population-based cluster sampling in 16 villages: 1,358 participants answered questions about routine activities and tsetse fly contact and received serologic testing. Seroprevalence in the surveyed area was 19.4% (95% confidence interval = 16.9%, 21.8%). We confirmed infection in 66% of seropositive persons who received one parasitologic examination and in 95% of those who had serial examinations of lymph node fluid and blood. Activities related to the civil war, such as temporary migration, were not associated with seropositive status. Since the previous population screening in 1988, the trypanosomiasis prevalence increased two orders of magnitude, and the proportion of villages affected increased from 54% to 100%. Our results suggest that there may be 5,000 cases in Tambura County. The absence of trypanosomiasis control for nearly a decade is a factor in the resurgence of the disease.