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To investigate the value of 3 novel autoantibodies [salivary protein 1 (SP1), carbonic anhydrase 6 (CA6), and parotid secretory protein (PSP)] in differentiating Sjögren's syndrome (SS)-related dry eye from non-SS dry eye.Forty-six dry eye patients with SS (SS dry eye), 14 dry eye patients without SS (non-SS dry eye), and 25 controls were included. The 2012 American College of Rheumatology classification criteria were used for the diagnosis of SS. After a detailed review of systems, the Ocular Surface Disease Index questionnaire, Schirmer test without anesthesia, tear film breakup time, and ocular surface staining were performed to assess dry eye. All participants underwent serological testing using a commercially available finger prick kit.Thirty-seven patients with SS (80.4%) had a positive traditional autoantibody and 28 (60.9%) had a positive novel autoantibody. Traditional autoantibodies were absent in all non-SS dry eye patients and controls. Novel autoantibodies were present in 7/14 (50%) non-SS dry eye patients and 4/25 (16%) controls. Among 3 novel autoantibodies, anti-CA6 was significantly more prevalent in the SS and non-SS dry eye groups than in controls (52.2% vs. 42.9% vs. 8.0%, P = 0.001). Dry eye patients with positive anti-CA6 alone were significantly younger than patients with only traditional autoantibodies. Anti-CA6 was associated with worse dry eye signs and symptoms.Anti-CA6 was the most prevalent novel autoantibody in patients with dry eye, and was associated with younger age and more severe disease. Longitudinal studies are needed to determine whether anti-CA6 is a marker for early SS or perhaps another form of an autoimmune dry eye disease.