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Aim: To compare central corneal thickness and endothelial cell loss after phacoemulsification with clear cornea and scleral tunnel incisions., Setting: Ophthalmology Department, Toronto Western Hospital, University of Toronto, Toronto, Ontario, Canada., Method: Fifty-one eyes of 51 patients were randomly assigned to one of the two study groups. All patients had central corneal thickness measured preoperatively and on post-op days 1, 7, 30 and 90. Specular microscopy was performed preoperatively and at 3 months after surgery., Results: Cumulative mean central endothelial cell count before surgery was 2,355 +/- 360 mm2 and 2,305 +/- 376 mm2 post-op. Mean percentage cell loss was 0.82% +/- 19.7%. For the scleral tunnel group it was 1.8% +/- 21.5%, and for the clear cornea group 0.13% +/- 18.3% (p>0.05). Two-way ANOVA demonstrated no effect of type of incision and surgeon on the endothelial cell loss. Pearson correlation coefficients between phaco power and cell loss calculated for each of the incisions and for each of the surgeons was not significant. Corneal thickness increased significantly in all measurements post-op, and returned to baseline by 3 months. There was no difference in the pachymetry change between the two study groups., Conclusions: Clear cornea and scleral tunnel incisions seem to result in no significant difference in endothelial cell loss and or central corneal thickness at 3 months post-op.