HighlightsA reverse line blot assay was used to estimate tick-borne haemoparasite prevalence in an intensively studied cohort of indigenous cattle in western Kenya.There were high prevalences of Theileria mutans (71.6%), T. velifera (62.8%), Anaplasma sp. Omatjenne (42.7%), A. bovis (39.9%), Theileria sp. (sable) (32.7%), T. parva (12.9%) and T. taurotragi (8.5%), with minor occurrences of eight other haemoparasites.The most prevalent haemoparasites were mostly present as coinfections, with strong associations between several of the Theileria parasites, in particular T. velifera with Theileria sp. sable and T. mutans, and T. parva with T. taurotragi.Comparison of RLB and serological results indicated that indigenous cattle seem capable of clearing infections of three pathogenic parasites (T. parva, A. marginale and B. bigemina), whereas infections with the mostly benign T. mutans are more persistent.