Purpose: To report the clinical efficacy of neodymium-doped yttrium aluminum garnet (Nd:YAG) laser iris cystotomy in iris cysts.Methods: We examined three eyes with primary iris cysts diagnosed by ultrasound biomicroscopy that had fewer cornea endothelial cells or reduced visual acuity due to an occluded visual axis. Nd:YAG laser cystotomy was done. The logarithm of the minimum angle of resolution (logMAR) visual acuity, intraocular pressure (IOP), and specular microscopy test at baseline and last follow-up were reviewed.Results: The average patient age was 54.0 ± 5.3 years; the mean follow-up was 11.7 ± 2.1 months. The baseline and final logMAR visual acuity were 0.23 ± 0.25 and 0.16 ± 0.15, respectively. Visual acuity improved, although not significantly (p = 0.317). The baseline and final IOP were 14.7 ± 2.3 and 13.7 ± 0.6 mmHg, respectively (p = 0.276). The corneal endothelial cell density (p = 0.109), hexagonality (p > 0.999), and coefficient of variation (p = 0.285) were not significantly different after treatment. There were no serious complications or recurrence.Conclusions: After Nd:YAG laser cystotomy, the cell density and morphology of corneal endothelial cells changed little. It can be considered an effective treatment when there is a decrease in corneal endothelial cells or occlusion of the visual axis.