Cattle market data shows that in Soroti, 54% of animals traded in the market in question originated from outside the district, from known sleeping sickness risk areas, and that up to 12.5% of the monthly imports from these areas may have been carriers of T.b. rhodesiense parasites. The theoretical impact that the alternative control options of mass chemotherapy or selective treatment following screening by microscopy would have had on reducing this risk are also considered, highlighting the limitations of field microscopy as a diagnostic tool for trypanosomiasis. Results from the case-control study showed that the epicentre of the outbreak which started in 1998 was Brookes Corner cattle market, the site through which most of the cattle in the restocking programme passed. Although residence in a village in proximity to the market was a highly significant risk factor for becoming a sleeping sickness case at the start of the outbreak, the average distance of cases to the market increased with time, indicating that the outbreak is expanding away from that point source. The results of the molecular analyses confirm that the parasites circulating in Soroti were similar to strains from the established sleeping sickness regions further south in Uganda, and shed further light on the nature of trypanosome population structures. The results are discussed in relation to the management of human trypanosomiasis in the cattle reservoir, with particular attention given to the implications of trypanosomiasis control policies aimed at livestock but which also benefit the health of the human population. Policies aimed at controlling disease in this way need to be made at a national level, and the importance of collaboration between medical and veterinary authorities for zoonotic disease control is stressed.