Aspergillosis is an uncommon disease in horses, but it can be fatal. We report two cases of systemic aspergillosis in foals that occurred in a short period in the same region of southern Brazil. In addition, a literature review of similar cases was also performed. Risk factors were attributed to an immunodepression by primary enterocolitis and corticosteroid treatment, the damage in the epithelium, and multiple antibacterial treatments, which allowed local fungal proliferation, tissue invasion and spread of infection, leading to death. Since the antemortem diagnosis of aspergillosis in foals is difficult, our report alerts equine veterinarians regarding the importance of suspecting and investigating fungal co-infections in complicated cases of enterocolitis.