A total of 363 cattle taken from six sub counties of Kashaari county were tested for presence of Theileria and Babesia species using reverse line blot hybridization assay (RLB). The prevalences of Theileria and Babesia species were found to be 19.8% (CI = 95%, 15.7-23.9%) and 0.6% (CI = 95%, -0.2-1.4%) respectively with at least 68% (CI = 95%, 63.2-72.8) dually infected with more than one Theileria sp. Theileria sp. detected include; T. parva, T. mutans, T. taurotragi, T. vilifera, T. buffeli, T. spp. (sable), T. spp. (buffalo) and T. bicornis at 24% (CI = 95%, 19.6-28.4% ), 18.4% (CI = 95%, 14.4-22.4%), 14% (CI = 95% , 10.4-17.6% ), 13.7% (CI = 95%, 10.2-17.2%), 12.6% (CI = 95%, 9.2-16.0%), 10.4% (CI = 95%, 7.26-13.54%), 4.4% (CI = 95%, 2.3-6.5%) and 3.8% (CI = 95%, 1.8-5.8%) respectively. The prevalences of different Theileria and Babesia species among different cattle age groups, breeds, management systems and sub county of origin are presented and discussed. A 2.5 times risk of infection associated with cross bred cattle (OR = 2.5, 95% CI; 1.44-4.49) compared to that of local and exotic breeds was observed on logistic regression. Regardless of type of cattle breed; rate of acaracide application, restriction of calf movement, restricted grazing (paddocking) and zero grazing were the most important parameters that determined the risk of infection with TBs. RLB detected infections in animals which were negative by Theileria and Babesia Genera specific PCR. Such animals had low parasitem ia that could not be detected by such non species-specific PCR. RLB is therefore a very sensitive and specific diagnostic tool that should be adopted in tick-borne hemoparasite epidemiological studies in Uganda.