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Equine piroplasmoses are enzootic parasitic diseases distributed worldwide with high incidence in tropical and subtropical regions. In Spain, there is insufficient epidemiological data about equine piroplasmoses. The main aim of the present study was therefore to estimate the prevalence of Theileria equi and Babesia caballi in five regions and obtain information about the risk factors. This study was conducted in the central and south-western regions of Spain, using indirect fluorescence antibody testing (IFAT) in 3,100 sera samples from apparently healthy horses of different ages, breeds, coat colours, genders and geographical locations. The overall seroprevalence was 52%, consisting of 44% seropositive for T. equi and 21% for B. caballi. There was a significant association between age (p < 0.0001), breed (p < 0.004), geographical location (p < 0.0001) and the seroprevalence, but neither the coat colour nor the gender was significantly associated with prevalence. In addition, it was proved that most of the geographic areas showed a moderate to high prevalence. The statistical κ value was used to compare the results obtained by the IFAT and the competitive enzyme-linked immunosorbent assay (cELISA) utilised to test some samples (n = 108) and showed a higher concordance for T. equi (κ = 0.68) than for B. caballi (κ = 0.22). Consequently, this revealed the importance of developing an appropriate technique to detect each haemoparasite.