Background: Equine piroplasmosis (EP) is a highly endemic protozoan disease of horses worldwide. While most horses in endemic areas are subclinically infected, the mechanisms leading to clinical outcome are vastly unknown. Moreover, since clinical signs of disease are not specific, and the prevalence in endemic areas is high, it is difficult to determine if EP is the cause of disease. To identify possible mechanisms leading to the clinical outcome in an endemic area, we compared parasite loads and genotypes in clinically and subclinically infected horses.Methods: Blood was collected from horses with clinical signs consistent with EP, and from apparently healthy horses from various locations. Packed cell volume (PCV) and total solids (TS) were measured from each sample. Quantitative and diagnostic PCR were used to quantify and classify EP infection in clinical and subclinical horses.Results: For both parasites, clinical cases were associated with low mean packed cell volume (PCV) and high mean parasite load (P<0.001), enabling to determine a cutoff value between clinically and subclinically infected horses. Theileria equi of subclinical horses classified into three different 18S rRNA genotypes: D (=23), A (n=12) and C (n=5), while all clinical cases classified as genotype A. The sequences of T. equi equi merozoite antigen-1 (ema-1) gene were fairly conserved and all classified as genotype A. The ema-2 sequences were analyzed with all currently published sequences and were mostly classified into one genotype (A) among the three resolved genotypes. Babesia caballi rhoptry associated protein-1 (rap-1) was classified into sub-genotypes A1 (n=14) and A2 (n=5) with no association to clinical outcome. Classification of the 18S rRNA gene (sub-genotypes B1 and B2) was in agreement with the rap-1 classification.Conclusions: The results of this study suggest that quantification of parasite loads of infected horses may be used to distinguish between clinical and subclinical cases. Additionally, we identified T. equi 18S rRNA genotype A to be associated with clinical disease. This finding emphasizes the importance of in-depth genetic characterization of T. equi genotypes to identify possible markers for virulence.