Horses have a low reproductive performance compared to other species. The aim of this study was to evaluate different sperm quality parameters in groups of fertile and subfertile stallions during the breeding and non-breeding season. Furthermore, molecular processes in response to different seasonal conditions as well as those are associated with male fertility were investigated. The comparison of transcript abundance between fertile and subfertile stallions and between breeding and non-breeding seasons provided a glimpse of the various functional pathways involved in stallion fertility.