To analyze the in vivo morphology of corneal cells and nerves in dry eye associated with primary (SSI) and secondary (SSII) Sjögren's syndrome and to study its relationship with the clinical evaluation. Thirty-five patients with SS and 20 age- and gender-matched control subjects were studied. Confocal microscopy was used to investigate corneal thickness, epithelial and stromal cellular density, and subbasal plexus morphology. Corneal central thickness was 514.74 +/- 19.85 microm in the SS group and 550 +/- 21.46 microm in the control group (P < 0.0001, t-test); stromal central thickness was 456.62 +/- 18.05 microm in the SS group and 487.35 +/- 20.40 microm in the control group (P < 0.0001). The density of the superficial epithelial cells in the SSI and SSII groups was 965.40 +/- 96.00 and 999.80 +/- 115.67 cells/mm(2), respectively, and 1488.55 +/- 133.74 cells/mm(2) in the control group (P < 0.001, ANOVA). The number of subbasal nerves was 3.34 +/- 0.76 in the SS group and 5.10 +/- 0.79 in the control group (P < 0.0001, t-test). The average grade of nerve tortuosity was 2.62 +/- 0.94 in the SS group and 1.20 +/- 0.70 in the control group (P < 0.0001). Statistically significant correlations were found between clinical data and confocal microscopy data. Corneal thickness, cells, and nerves show morphologic changes in patients with dry eye associated with SS. The in vivo confocal study of these alterations may be important in better understanding the complexity of the ocular surface morphofunctional unit and the potentials of therapeutic approaches for the control of the phlogistic process and neuroprotection.