Between August and October 2000, a cross-sectional study was conducted in smallholder dairy farms in Mbale District, Uganda to assess the prevalence of ticks and tick-borne diseases under different grazing systems and agro-ecological zones and understand the circumstances under which farmers operated. A questionnaire was administered to obtain information on dairy farm circumstances and practices. A total of 102 farms were visited and sera and ticks were collected from 478 animals. Sero-prevalence of tick-borne diseases was determined using an enzyme-linked immunoassay. Acaricides were used indiscriminately but the intensity of their use varied with the grazing system and zone. Cattle from different farms mixed for various reasons. During the dry seasons farmers have to get additional fodder from outside their farms that can result in importation of ticks. The prevalence of ticks and serum antibodies to tick-borne infections differed across the grazing systems and zones. The highest serum antibody prevalence (>60%) was recorded in the lowland zone under the free range and tethering grazing systems. The lowest tick challenge and serum antibody levels (<50%) were recorded in the midland and upland zones under a zero-grazing system. These findings suggest that endemic stability to East Coast Fever, babesiosis and anaplasmosis is most likely to have existed in the lowland zone, particularly, under the tethering and free-range grazing systems. Also, endemic stability for babesiosis existed in the upland zones. Endemic instability for East Coast Fever existed in the midland and upland zones. These structured observational studies are instrumental in planning of control strategies for ticks and tick borne diseases since production systems and the cattle population at high risk of the diseases in the district have been identified.