Background: Mitomycin C is an antimetabolite and affects corneal endothelial cells as measured by noncontact specular microscopy after trabeculectomy with mitomycin-C (MMC). Objective: To evaluate the corneal endothelial cells changes after trabeculectomy with MMC. Patients and methods: Patients were categorized into 2 groups, group A(25 eyes) were managed by trabeculectomy with mitomycin-C injection, group B (25 eyes) were managed by trabeculectomy with mitomycin-C sponge-applied technique which was carried out on patients attending at Ophthalmology Department of Al-Azhar University Hospitals from March 2019 to February 2021. Follow-up by specular microscopy preoperatively and 1 month and 6 months postoperatively to evaluate corneal endothelial cells density and morphological changes. Results: There was a significant reduction in the endothelial cell density and percentage of hexagonal cells and increased variation in cell size in the two studied groups after 1 month and 6 months compared with preoperative values. With no differences between the two studied groups. Conclusion: Trabeculectomy with both MMC injection and sponge applied caused a significant loss of the corneal endothelial cells intraoperatively or at the early postoperative period. Progressive cell losses due to MMC were not a major concern.