Purpose: To study the endothelial integrity, count and morphology in keratoconus patients, and correlate the endothelial changes to the stage of keratoconus.Methods: Forty eyes of 29 patients diagnosed with keratoconus were enrolled in the study. Corneal endothelium was evaluated using specular microscopy. Eyes were classified into 2 subgroups according to the median of the thinnest location;Group A: Thinnest location ≤ median of the thinnest location, Group B: Thinnest location > median of the thinnest location .Eyes were also classified into stages 1, 2 and 3 of Amsler’s classification according to the mean Keratometry (Km) and pachymetry readings obtained from computerized tomography.Results: Comparing group A with group B; lower endothelial cell density in group A than group B (2327.30 ± 620.84 cells/mm2 vs. 2411.15 ± 333.94 cells/mm2,P꞊ 0.59 ),lower coefficient of variation in group A than group B (34.70 ± 9.937 vs. 36.40 ± 7.95,P꞊ 0.55 ),higher percent of hexagonality in group A than group B (60.89 ± 12.02 % vs. 57.29 ± 13.82 % ,P꞊ 0.41).Eleven eyes (27.5 %) had stage 1 keratoconus, 17 eyes (42.5 %) had stage 2 keratoconus ,and 12 eyes (30 %) had stage 3 keratoconus .Cases with stage 4 keratoconus were excluded. The endothelial cell density in stage 1 was (2404.46 ± 344.68 cells/mm2),in stage 2 (2455.41± 330.39 cells/mm2), in stage 3 (2214.83 ± 747.84 cells/mm2 ).The coefficient of variation in stage 1 was (35.55 ± 9.66),in stage 2 (34.82 ± 6.23), in stage 3 (36.58 ± 11.797 ).The percentage of hexagonality in stage 1 was (61.56 ± 15.78 %),in stage 2 (58.5 ± 12.39 %),in stage 3 (58.27 ± 11.86%).The Correlation coefficient between stages and cell density was 0.018 (P = 0.91), between stages and coefficient of variation was -0.011 (P = 0.94), and between stages and percent of hexagonality was -0.112 (P =0.51).Conclusion: Keratoconus up to stage 3 does not significantly affect the corneal endothelium, as measured by specular microscopy.