PurposeTo investigate the risk factors for corneal endothelial cell density (ECD) loss of two types of iris-fixated phakic intraocular lenses (pIOL) and indicate the cutoff values for preventing irreversible ECD loss after explantation. DesignThe retrospective, comparative, clinical cohort study MethodsTotal 114 eyes of 61 patients were included in this study. Fifty-five eyes with Artisan pIOL and 59 eyes with Artiflex pIOL had undergone explantation of pIOLs due to continuous ECD loss. Correlation analysis was performed to assess the ocular parameters associated with ECD loss. Receiver operating characteristic (ROC) curve was performed to set cutoff values of ocular parameters to prevent ECD loss after explantation. ResultThe mean ECD before explantation was 1637 cells/mm2 in Artisan group and 1769 cells/mm2 in Artiflex group. The distance of cornea endothelium to IOL center and edges were all significantly higher in Artisan group (p <0.05). The risk factor of decreased ECD in Artisan group were small anterior chamber angle (ACA), and distance of nasal edge of IOL to endothelium and iris fixation to nasal limbus distance, and differences of fixation length. In Artiflex group, ACA, distance of nasal edge of IOL to endothelium, both limbus to IOL fixation length, fixation length, iris pigmentation grading were the risk factors. At 1 year after the pIOL removal, the population demonstrating ΔECD >10% were significantly higher in Artisan group than Artiflex group (p <0.05). In ROC curve analysis, the cutoff value of preoperative ECD to prevent significant post-explantation ECD loss was 1683.5 cells/mm2 in Artisan group and 1648 cells/mm2 in Artiflex group. ConclusionThis study examined the existing explantation guidelines for these lenses. In analyzing the longterm prognosis of cornea ECD with Iris-fixated phakic intraocular lens, it is important to identify the relevant anatomical factors. Small ACA, and short distances from IOL to endothelium and from limbus to iris fixation especially in the nasaSSSl region were significant risk factors to continuous ECD loss in both lenses. To minimize irreversible ECD loss after explantation, it is important to determine the optimal period of explantation by observing both ECD and structural changes.