In recent years, gastric ulceration has been recognized as a common, possibly performance-limiting disease, of adult horses. The aim of this study was to compare endoscopic features, histological diagnosis, and mRNA levels of various cytokines (TNF-α, IL-1β, and IL-13) from horse gastric biopsies. Eleven horses suffering from equine gastric ulcer syndrome and seven horses with normal histological gastric features were assessed. No correlation between endoscopic features and histology (i.e., the gold standard) was observed. Based on histological diagnosis, a significant (p < 0.05) increase in cytokine mRNA levels (specifically, TNF-α and IL-13) was observed in horses affected by equine ulcerative gastric syndrome.