PURPOSE: We sought to demonstrate the impact of Clic6 deficiency in the retina and RPE of C57BL/6N mice that are homozygous for the Crb1rd8 mutation. METHODS: Six Clic6-/- and six age-matched wild-type mice were used. Ophthalmic examination, ERG, and retinal optical coherence tomography were performed for clinical phenotyping. The mice were euthanized, and the eyes were processed for hematoxylin and eosin stain, immunohistochemistry, and transmission electron microscopy. Additionally, adult nonhuman primate and fetal human retinas were used for immunohistochemistry. RESULTS: Both Clic6-/- and wild-type mice showed retinal lamination defects on optical coherence tomography and hematoxylin and eosin staining with a significantly greater number of lesions identified in Clic6-/- mice. No significant differences in ERG parameters were identified between genotypes. The expression of ezrin/radixin/moesin seemed to be flat and blunted at the apical RPE surface in Clic6-/- vs. wild-type mice. On transmission electron microscopy, Clic6-/- mice showed broadened and stout RPE microvilli with a significantly decreased apical microvilli height and significantly increased width of each RPE microvillus. Although the height of the RPE cells and basal infoldings and pigment granule density did not differ significantly, phagosome density was significantly greater in Clic6-/- mice. Both CLIC6 and ezrin/radixin/moesin were expressed in the RPE of adult nonhuman primate and fetal human tissues. CONCLUSIONS: Clic6 deficiency induced aberrant RPE microvilli leading to a decreased intimacy between the RPE and photoreceptors and worsened the Crb1rd8 mutation phenotype that was inherent in C57BL/6N mice. CLIC6 may have a potential role in RPE dysfunction across species, including humans.