The urgent need to improve livestock productivity in sub-Saharan Africa in order to keep pace with expected increases in demand for meat and milk is very topical. Breed improvement provides key entry points for increasing productivity in cattle populations. However, there are tendencies for breed improvement programs to focus on single, market driven traits such as milk or meat production in isolation of environmental constraints and broader livestock system functions which cattle assume in developing countries. This potentially leads to genotypes that are not well adapted to the environment and not capable of performing the multiple roles that cattle assume in cattle production systems of developing countries. In developing countries, many important functions of livestock are embedded in non-tradable traits that are neither captured in economic analysis nor considered in livestock improvement programs. This study evaluates preferences of cattle keepers in pastoral and crop- livestock systems of selected sites in Kenya for various cattle traits, focusing attention on trypanotolerance and employing choice modelling techniques. These systems are characterized by low input management, harsh environmental conditions and prevalence of various cattle diseases. Trypanosomosis is a serious disease constraint in these systems. The results indicate that farmer preferences for cattle traits are influenced by various factors including cultural practices, production system characteristics and environmental conditions, especially in relation to disease prevalence and availability of cattle feeds.