We determined the prevalence of tuberculosis and brucellosis reactors in the dairy herds in the Mbarara district of Uganda in 2002. This is one of the most important dairy-production areas of the country and includes both pastoral and agro-pastoral zones. A total of 340 (of 11,995) randomly selected herds were tested for tuberculosis, using the intradermal tuberculosis-skin test and 315 (of 10,562) herds tested for brucellosis using the serum Rose Bengal test. The herd prevalence for tuberculosis reactors was 74.1% (95% confidence intervals 69, 78), the individual-animal prevalence was of 6.0% (5.6, 6.5) and within-herd range was 1-50% (up to 100% if suspicious reactors were included). The herd prevalence for brucellosis was 55.6% (50, 61.2) individual-animal prevalence 15.8% (14.8, 16.7) and within-herd range 1-90%. The reactor prevalence increased with the age of the animals for both tuberculosis and brucellosis. Tuberculosis reactor prevalences were higher in animals from the agro-pastoral zone. However, the individual-animal and herd prevalences of brucellosis seroprevalences were higher in the pastoral zone.