Objective: To compare the effects of transverse versus torsional phacoemulsification by using the biaxial microincision cata ract surgery technique on corneal structures and clear corneal incision (CCI) morphology. Material and Methods: We evaluated comparative case series of patients with moderate density nuclear cataracts who un derwent biaxial microincision transverse or torsional phacoemulsifica tion. Seventy patients have included in the study and they were divided into 2 groups: transverse and torsional. The main outcome measures included, corrected distance visual acuity, central corneal thickness, central corneal endothelial cell density, endothelial cell loss (ECL), and changes in the CCI morphology. Results: Each group comprised 35 (35 eyes) patients. Epithelial misalignment on the CCI morphology was highly significantly meaningful with the transverse group on the po stoperative first day (p<0.001). Descemet membrane detachment on the first day postoperatively was high in both groups, especially in the transverse group, but the difference was not statistically significant (p=0.073). In the postoperative 3rd month, the mean ECL was 23.6% in the transverse group, and 19.0% in the torsional group, and there was no statistically significant difference between groups (p=0.187). Con clusion: In biaxial microincision cataract surgery, the corneal damage caused by transverse phacoemulsification seems to be higher compared to the torsional mode.