Piroplasmosis and trypanosomiasis are debilitating diseases of great economic impact on the equine industry of Latin America. Considering the lack of studies in the northeastern part of Colombia, this study aimed to determine the epidemiological, clinical and genetic features associated with infection of the Babesia, Theileria, and Trypanosoma species in horses from this geographical area. Two hundred and eighty horses from the Arauca, Meta, and Santander departments were molecularly analyzed for infection with Babesia caballi, Theileria equi, Trypanosoma evansi, and Trypanosoma vivax. Furthermore, clinical, epidemiological and entomological analyses were performed on the data sets. Molecular analysis showed 25.7% and 3.9% prevalence for T. equi and T. evansi, respectively, without positive animals for B. caballi and T. vivax. There were no differences in the prevalence of T. equi between departments, whereas T. evansi was detected exclusively in Santander. A total of 633 ticks were collected from 72 horses across the three departments, with 84.7% corresponding to Dermacentor nitens, 10.9% to Amblyomma cajennense (sensu lato) (s.l). and 4.4% to Rhipicephalus microplus. For T. equi, genetic analyses showed that Colombian isolates belong to genotype C of species, along with sequences of Brazil and Mexico. Epidemiological analysis revealed a significant association between tick infestation and lack of vector control with molecular infection of T. equi, whereas clinical analysis revealed a significant reduction in packed cell volume, red blood cells, and mean corpuscular volume in positive animals to this pathogen. Furthermore, molecular infection by T. evansi was associated with epidemiological characteristics in the Santander department. In conclusion, our analysis revealed a moderate infection rate by T. equi of genotype C in horses from northeastern Colombia, which affects their clinical conditions. Control of ticks and treatment of symptomatic animals should be considered to reduce the economic impact associated with these infections in the equine industry.