A comparative analysis of endothelial cell loss was done after manual small incision cataract surgery and phacoemulsification with 50 patients in each group in a tertiary care eye hospital in India. Follow up was done upto 8 weeks for visual acuity, mean endothelial cell density, corneal thickness and change in hexagonality. Analysis was done on TOPCON- 3000P specular microscope. Males and females were equally distributed mainly in 51-60 years of age group. The visual acuity in group A (phacoemulsification) was 6/6 in 68% patients while in group B it was 6/6 in 40% patients. There was more decrease in mean endothelial cell density in group A (phacoemulsification) 4.24% vs 3.87%. Corneal edema occurred in both the groups initially but was not statistically significant. The overall loss of hexagonal cells is not statistically significant between phacoemulsification and manual small incision cataract surgery. All through our study, there was more corneal edema, endothelial cell loss and decrease in hexagonality in phacoemulsification group. However, the difference was not statistically significant. Hence, both the surgeries are safe pertaining to corneal endothelial health