PURPOSE: To quantify changes in endothelial cell counts and corneal thickness measurements in patients having standard phacoemulsification compared with femtosecond laser-assisted cataract removal. SETTING: Ruhr University Eye Clinic, Bochum, Germany. DESIGN: Prospective randomized intraindividual cohort study. METHODS: One eye of each patient had standard phacoemulsification (control group) and the other eye had femtosecond laser-assisted phacoemulsification (study group), both with intraocular lens implantation. Pulsed ultrasound energy was used for phacoemulsification. Noncontact endothelial cell microscopy and corneal pachymetry were performed preoperatively and 1 day, 3 to 4 days, 7 to 10 days, 50 to 60 days, and 90 to 100 days postoperatively. RESULTS: The mean endothelial cell loss was 7.9% +/- 7.8% (SD) 1 week postoperatively and 8.1% +/- 8.1% 3 months postoperatively in the study group and 12.1% +/- 7.3% and 13.7% +/- 8.4%, respectively, in the control group. The mean relative change in corneal thickness from the preoperative values was -0.0% +/- 1.9% at 1 day, 2.8% +/- 1.8% at 1 week, and 3.3% +/- 1.7% at 3 months in the study group and -0.9% +/- 2.3%, 2.4% +/- 1.5%, and 3.2% +/- 1.4%, respectively, in the control group. CONCLUSION: The femtosecond laser did not add to the endothelial damage caused by cataract surgery and might be beneficial in eyes with low preoperative endothelial cell values (eg, cornea guttata cases).