This research was performed to study the prevalence of antibodies against Babesia equi in horses of the northern region of Rio Grande do Sul state, using ELISA and indirect immunofluorescence antibody test (IFA). The total sera sample was 380, this number was considered as statistically representative of the population, as determined by mathematical model. The prevalence of B. equi was 31.6% and 35.8% by ELISA and IFA, respectively. The concordance between the assays was 0.87 (indices kappa), which is considered an optimal result. The results did not show any significant statistical difference (P < 0.05) between sex, age and horses breed. The results of this study allowed the characterization of the northern region of Rio Grande do Sul as an instable enzootic area for B. equi, which indicates a potential risk of economic losses caused by babesiosis outbreaks, especially for sensible horses from non enzootic areas or even born is the studied region.