Although livestock forms a very important component of the livelihoods of rural populations of developing countries, productivity remains very low. Livestock keepers are beset by various constraints. In sub-Saharan Africa, cattle are exposed to a number of tropical diseases and other environmental stresses. Breed improvement programs provides key entry points for increasing productivity in cattle populations, especially those plagued by animal diseases. However, breed improvement programs have tended to focus on single, market-driven production traits in isolation of broader livestock system functions. This potentially leads to genotypes that are not well adapted to the environment and not suitable for performing the multiple roles of cattle in developing countries. In order to design a sustainable breed improvement program, farmer preferences for cattle traits need to be integrated into the breeding objective. To explore preferences for cattle traits by cattle keepers, data are used from a choice experiment household survey from a sample of 507 cattle keeping households in trypanosomosis challenge areas in Kenya and Ethiopia. A multinomial logit and mixed logit models are applied to estimate the economic values of preferred cattle traits. The results show existence of preference heterogeneity for cattle traits based on cattle production systems. Further, the results suggest that important traits in developing breed improvement programs should include trypanotolerance, fitness to traction, drought tolerance and fecundity, drawing implications on conservation of breeds which possess these traits.