Background The tsetse-transmitted African trypanosomiases affect humans and animals. Trypanosoma. brucei rhodesiense sleeping sickness, or human African trypanosomiasis is a zoonosis, for which cattle are the main reservoir of infection in south-eastern Uganda. Transmission of human and animal infective trypanosomes can be reduced by the application of deltamethrin insecticide to the belly and legs of cattle, thus reducing tsetse fly populations. Alongside an epidemiological study in southeastern Uganda, a farm level assessment was done to calculate the average and incremental benefit-cost ratios of spraying different proportions of the village cattle population using this restricted application protocol.Method A study comprising 2,400 semi-structured interviews was undertaken over a period of 18 months. Financial data on household income and expenditure on cattle provided the basis for the marginal analyses. The benefit of RAP to farmers was assessed using gross margin analysis whereas the costs were obtained from expenses incurred by farmers in participating in the RAP intervention. Subsequently, the RAP intervention villages were compared with a control village to determine the average and incremental benefit-cost ratio across all households.Results The benefit-cost analysis of spraying 25%, 50% and 75% of the cattle population yielded benefit-cost ratios of 6.22, 5.56 and 4.46. The incremental benefit-cost ratios from spraying each additional 25% of the population cattle were 14.32, 3.97 and 0.79 respectively, showing a very high return on investment in spraying 25% of the population, with returns reducing thereafter.Conclusion Comparing the gross margins per bovine of applying RAP to different proportions of the cattle population to a pre-intervention situation and a control, the study found that increasing the proportion of cattle sprayed yielded increasing benefits to farmers, but that these benefits were subject to diminishing returns. Given the high proportion of draft males in the cattle population (37%) their important contribution to livestock output and farmers’ preference for treating these animals, from a practical viewpoint this study recommends spraying only draft cattle to control trypanosomiasis in this area, although in areas or households with a lower proportion of draft males, farmers could be advised to also include cows.