A resurgence of sleeping sickness developed in southern Sudan during the past decade. Prevalence of confirmed Trypanosoma brucei gambiense infection in humans now exceeds 5% in several foci. From 1997 to 1999, trypanosomiasis control programmes in three counties of Western Equatoria Province detected 3785 new cases among 67 181 persons screened. A major contributing factor in the re-emergence of epidemic sleeping sickness was the lack of active case-finding throughout the 1990s. Although the situation is improving in sites where trypanosomiasis programmes have been recently implemented, co-ordination and additional international assistance are needed to bring sleeping sickness under control in Sudan.