Purpose To determine the structure and morphology of corneal endothelial cell layer in patients with acute anterior uveitis. Methods Thirty-four eyes of 34 acute anterior uveitis patients and 34 eyes of 34 healthy subjects were included. Mean cell density, coefficient of variation, maximum cell area, minimum cell area, average cell area and hexagonality ratio values were evaluated by non-contact specular microscopy. Parameters recorded in both groups were compared. Results The mean maximum cell area was 1054,44 +/- 251,14 mu m(2), minimum cell area was 152.29 +/- 53.65 mu m(2) and average cell area was 386.91 +/- 41.73 mu m(2) in acute anterior uveitis group and the mean maximum cell area was 1057.65 +/- 261.23 mu m(2), minimum cell area was 147.26 +/- 20.45 mu m(2) and average cell area was 383.53 +/- 43.12 mu m(2) in the control group. There were no significant differences between the two groups in terms of maximum, minimum and average cell area (respectively, p = 0.080, p = 0.72, p = 0.62, p = 0.67). The mean cell density was 2607.74 +/- 277.63 cells/ mu m(2) in acute anterior uveitis group and 2669.35 +/- 265.22 cells/mu m(2) in the control group. (p = 0.358). In acute anterior uveitis group the mean coefficient of variation was 31.68 +/- 8.16, hexagonality ratio was 63.85 +/- 11.14 and mean central corneal thickness was 571.47 +/- 55.99 mu m; in control group the mean coefficient of variation was 25.29 +/- 3.00, mean hexagonality ratio was 72.6 +/- 4.80% and mean central corneal thickness was 534.82 +/- 33.84 mu m. Statistically significant differences were seen between the two groups (respectively, P = 0,00, P = 0,00, P = 0.02). Conclusion The mean central corneal thickness and coefficient of variation values were found higher, and the hexagonality ratio was found lower in acute anterior uveitis group. Our findings suggest that intraocular inflammation in anterior chamber negatively affects the endothelial function in patients with acute anterior uveitis.