Trypanosome infections were monitored in three species of tsetse fly (Glossina pallidipes Austen, G. morsitans centralis Machado, and G. brevipalpis News-tead) at four locations in the Kagera River region of Rwanda from May 1989 to September 1990. Two of the four areas (Mpanga Ranch and Bukora Ranch) were subjected to tsetse fly suppression operations with odour-baited traps. Proboscis infections of the Trypanosoma congolense and T. vivax types accounted for roughly equal numbers of the 207 mature infections detected (3.8%). Variation in infection rates was area-specific rather than tsetse species-specific. Order of magnitude differences in tsetse fly densities among areas were not correlated with differences in infection rates at the start of tsetse fly suppression operations. Similarly, declines in population density on both control and experimental areas were not associated with significant changes in infection rates. The prevalence of trypanosomiasis in cattle at Bukora Ranch was not affected by a roughly 90% reduction in Glossina densities. T. congolense accounted for 79% of the infections at an overall prevalence rate of 5.5%. Trypanosomiasis in cattle persisted at extremely low densities of about 0.1 fly/trap/day. Treatment of cattle with diminazene aceturate (BereniR) suggested that many T. congolense parasites were drug resistant, and hence, were cycling among cattle due to the few Glossina present.