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To quantify the morphology of corneal basal epithelium and subbasal nerves and to evaluate the ocular surface alterations in patients with fibromyalgia (FM).Patients with FM (n = 34) and healthy controls (n = 42) were enrolled. All participants underwent ocular surface tests in the following order: corneal sensitivity, tear film breakup time, lissamine green staining, Schirmer test, and the Ocular Surface Disease Index questionnaire. Basal epithelial cells and subbasal nerves were evaluated using in vivo confocal microscopy (IVCM). Demographic characteristics, Visual Analog Scale for Pain (VAS), American College of Rheumatology 1990, the Widespread Pain Index (WPI), and the Symptom Impact Questionnaire (SIQR) scores of patients with FM were obtained.Corneal sensitivity was 0.4 g/mm2 (fiber length: 6.0 cm) in all eyes. Patients with FM had a higher Ocular Surface Disease Index (42.2 ± 18.9 vs. 1.2 ± 1.7, P < 0.001), higher lissamine green staining scores (0.5 ± 0.5 vs. 0.05 ± 0.2, P < 0.001), and lower tear breakup time scores (9.0 ± 3.6 vs. 10.3 ± 1.5, P = 0.003) than the controls. Basal epithelial cell density (2709 ± 494 vs. 4491 ± 724), total nerve density (1563 ± 620 vs. 2545 ± 973), long nerve fibers (3.4 ± 1.3 vs. 4.5 ± 1.0), and the number of nerves (5.0 ± 1.8 vs. 10.3 ± 2.1) were all lower in patients with FM compared with those of the controls (P < 0.001 for all). There was a statistically significant negative correlation between the WPI score and Schirmer test results (rho = −0.374, P = 0.03) and between WPI and total nerve density (rho = −0.334, P = 0.054).To the best of our knowledge, this is the first study that evaluated ocular surface alterations in the context of corneal IVCM characteristics. Patients with FM should be evaluated in terms of ocular surface diseases. IVCM may be used in FM to assess small fiber neuropathy.