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Purpose: To compare Endothelial cell(EC) loss following Phacoemulsification (PKE) in pupils of different sizes. Methods: A prospective double masked observational study in which a total of 150 eyes of 150 patients between 50 & 70 years of age with senile cataract of nuclear sclerosis grade II were enrolled. Patients were allocated into three groups of 50 eyes each in Group A (pupil size <5 mm), Group B (pupil size 5–7 mm) and Group C (pupil size >7 mm). Pupillary size was measured by determining the height of slit on slit-lamp biomicroscope examination. PKE was done by the same expert surgeon using vertical chop technique and a foldable intraocular lens was implanted in the capsular bag. Corneal EC count and pachymetry were performed twice and average of 2 readings was taken for the purpose of this study. Measurements were taken preoperatively and postoperatively on day 1, day 7 and day 30. Results: The mean EC count loss on postoperative day 1 in Group A was 19.45%, Group B 14.89%, Group C 10.19% with statistical significant difference between Group A and Group B, as also Group A and Group C. The difference was not significant between Group B and Group C, though there was a fall in EC count in Group C as well. Increase in corneal thickness on postoperative day 1 in group A was 5.43%, Group B 3.55%, Group C 2.14% with statistical significant difference between Group A and Group B, as also Group A and Group C with no difference in Group B and Group C. Conclusion: PKE done in eyes with maximal pupillary dilatation of <5 mm causes a greater EC loss and results in thicker corneas postoperatively as compared to eyes with pupillary dilatation of >5 mm at the end of one month.