PurposeTo study the factors affecting the corneal endothelium after selective laser trabeculoplasty (SLT) in primary open angle glaucoma (POAG) and primary angle closure glaucoma (PACG).MethodThis prospective interventional study included 56 patients (56 eyes) with POAG and 55 patients (55 eyes) with PACG. All participants received a standard SLT session. Patients with PACG were pretreated with laser peripheral iridotomy for at least 2 months before SLT. Corneal endothelium cell count (ECC), pleomorphism and polymegathism were measured before SLT, as well as at the increments of 1 hour, 1 day, 1 week, 1 month, 3 months and 6 months following SLT using confocal microscopy. A multiple regression analysis was applied to detect the factors affecting the ECC in the long-term post-SLT period.ResultsIn both groups, the mean ECC significantly decreased from the baseline after SLT. While in POAG, corneal endothelium recovered within 1 month, in PACG, its damage persisted throughout the whole follow-up period.According to the multiple analysis, baseline ECC (β=0.891, p=0.000 in POAG and β=0.706, p=0.000 in PACG) and age (β=−0.227, p=0.000 in POAG and β=−0.196, p=0.000 in PACG) were the common risk factors affecting ECC in both glaucoma forms, while the initial anterior chamber depth (β=0.254, p=0.000), only in PACG. The duration of glaucoma treatment (β=−0.317, p=0.043 in POAG and β=−0.302, p=0.047 in PACG) and pigmented deposits on the corneal endothelium in PACG (β=−0.326, p=0.019) were the risk factors determined in the univariate analysis.ConclusionAge and the baseline ECC are the risk factors for corneal endothelium damage after SLT in POAG and PACG. Shallow anterior chamber may affect corneal endothelium in PACG. These data should be considered when choosing an algorithm for glaucoma treatment.