Equine Gastric Ulcer Syndrome (EGUS) is a widespread disease with a very high prevalence and importance in horses. It includes two conditions: Equine squamous gastric disease (ESGD), linked to acid disturbances, and Equine Glandular Gastric Disease (EGGD), associated with inflammation and immune system issues. In saliva, increased levels of immunological markers have been observed in this disease, indicating immune system involvement. In addition, changes in biomarkers of oxidative stress have been described. In horses, IgG and IgA are proteins that appear in saliva and serum and are considered to be the major proteins in specific immunity; however, their levels in horses with EGUS have not been previously studied. This report aims to evaluate IgG and IgA concentrations in the saliva and serum of horses with EGUS, measured by automated assays, and compare them with other biomarkers of the immune and oxidative stress system. This work validated the IgG and IgA assays in saliva and showed that IgA significantly increased in the saliva of horses with EGUS. When the correlation between IgG and IgA and other biomarkers of immune system issues and oxidative stress such as ADA, S100 A8-A9 (calprotectin), S100 A12 (calgranulin), uric acid, FRAS, and AOPP was studied, IgA in saliva showed a significant moderate correlation with adenosine deaminase, indicating its possible involvement in the immune reaction occurring in EGUS.