Background: Femtosecond Laser Assisted Cataract Surgery has benefits and drawbacks, our work was to study its effects on the corneal integrity. Objectives: To study the effect of femtosecond laser assisted cataract surgery on the corneal integrity in comparison with phacoemulsification.   Patients and methods; This prospective comparative randomized controlled study was done at Cortoba eye center, Cairo. It was conducted on 40 eyes suffering from cataract graded from 2 to 4. They were divided into 2 equal groups. Group (A) femtosecond laser assisted cataract surgery was done using Victus Femtosecond Laser Platform (Bausch and Lomb). Group (B) conventional phacoemulsification was done using Alcon Infiniti Phaco Machine. Full preoperative ophthalmological examination, best corrected visual acuity (BCVA), corneal thickness and endothelial cell count were done and repeated postoperatively. Main outcome measures included visual acuity, corneal oedema, corneal thickness, and endothelial cell count. Data was collected and statistically analyzed. Results: Regarding corneal thickness; there was no significant difference between groups and it significantly increased in both groups. Corneal endothelial cell count in Group B was significantly lower after one month and it significantly decreased in both groups but more in group B. Conclusion: Femtosecond laser assisted cataract has a transient corneal edema and loss of endothelial cell count with less effects on the corneal integrity than phacoemulsification.