Sjögren's Syndrome (SS) is an autoimmune exocrinopathy characterized by the progressive damage of salivary and lacrimal glands associated with lymphocytic infiltration. It can be defined as primary SS (pSS) or associated/secondary SS (sSS) if combined with another systemic autoimmune disease. Identifying new non-invasive biomarkers for SS diagnosis remains a challenge, and alterations in saliva composition reported in patients turn this fluid into a source of potential biomarkers. To examine the overall panorama of proteins in saliva, samples of control, pSS, and sSS individuals were analyzed by gel-based LC-MS/MS.