AIM: To evaluate the effect of torsional mode phacoemulsification on central corneal thickness, corneal endothelial cell density, and morphology in eyes with/without pseudoexfoliation (PEX) syndrome. METHODS: Fourty-two consecutive patients with and 42 patients without PEX as a control group scheduled for cataract surgery was studied. Phacoemulsification, using OZiL IP system, was performed with quick chop technique. Using noncontact specular microscopy, the central endothelial cell density (ECD), coefficient of variation, percentage of hexagonal cells, and the central corneal thickness (CCT) were evaluated preoperatively and postoperatively at 1, 7 and 30d. RESULTS: The ECD in PEX syndrome was statistically significantly lower than that in the control group preoperatively and postoperatively (P≤0.001). Percentage change in ECD was statistically significantly higher in PEX than that in control group after surgery follow up (P≤0.04). There was no statistically significant difference between both groups comparing percentage of hexagonal cells and coefficient of variation in the cell size before and after the surgery. At 1 and 7d after surgery, percentage change in CCT was statistically significantly higher in PEX group than that in the control group (P≤0.041). CONCLUSION: Although torsional mode phacoemulsification and intraocular lens (IOL) implantation provided a safe and favorable surgical outcome in patients with/without PEX, torsional phacoemulsification led to significantly higher ECD loss in the PEX group than that in the control group during the whole follow up period. In addition, more corneal swelling in the PEX group than that in the control group during the early postoperative period has indicated that the corneal endothelium, in presence of PEX endotheliopathy, seems to be more susceptible to the effects of phacoemulsification surgery in eyes with PEX. The increased risk of anterior chamber manipulations in patients with PEX should be taken into account for an increased risk of bullous keratopathy.