Polymorphisms in MSTN have previously been associated with equine performance. Therefore, the aim of this study was to identify variants in MSTN intron 1 in 16 Brazilian sport horses selected for competition in eventing and their possible effects of selection on performance. Among the nine variants identified, eight had already been reported in previous studies or genomic databases, although they showed differences in frequencies when compared with other horse breeds. Moreover, a new mutation was identified in two horses, both in heterozygous form. Considering the absence of molecular studies in this valuable Brazilian breed, these findings represent an important contribution to the characterization of its genetic profile and may possibly aid in further genotype-phenotype association studies.