To compare short-term changes in corneal endothelial cells after gonioscopy-assisted transluminal trabeculotomy(GATT). This retrospective comparative study included 138 patients(138 eyes), and 98 of these patients underwent GATT procedure and 40 underwent SLT procedure as a control group. Changes in the corneal endothelium in patients who underwent GATT and SLT were analyzed retrospectively. Endothelial changes in the central cornea were examined using specular microscopy before and 6 months after the GATT and SLT procedure. Intraocular pressure(IOP), number of glaucoma medications, and side effects were evaluated at visits before and after two methods. One hundred and thirty-eight eyes of 138 patients with a mean age of 62.9±12.7 years in the SLT group and 62.5±11.8 years in the GATT group were included in this study. Pre-procedure mean ± SD IOP was 27.7±3.6 mmHg and 27.4±5.3 mmHg (p=0.173) 2.8±0.5 and 2.9±0.8 (p=0.204) glaucoma drugs are in the SLT and GATT group, respectively. The mean corneal endothelial cell density (CECD) in the SLT group was 2433.1±581.4 cells/mm2 before the procedure and 2435.1±585 cells/mm2 6 months after the procedure, a change of 0.1±0.6% which was not statistically significant (p>0.967).The mean CECD at baseline in the GATT group was 2443.4±508.2 cells/mm2 and decreased to 2290.2±527.7 cells/mm2 6 months after this procedure, representing a cell loss of 6,2±9,1% (p<0.001). GATT caused more CECD damage than SLT at the sixth month after the procedure. Considering the loss of CECD in candidates for GATT, sufficient number of endothelial cells in the central cornea is recommended.