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A possible association has been reported between exfoliation syndrome (EX) and various ocular and systemic vascular disorders; however, it is unclear if there is an association between EX and central retinal vein occlusion (CRVO). Because latent deposits of exfoliation materials might not be recognized during slit-lamp examination, an ocular biopsy is required to establish a precise diagnosis. We evaluated a possible association between EX and CRVO usinglysyl oxidase-like 1(LOXL1) gene variants as alternative markers for EX.The allelic and genotypic frequencies of threeLOXL1variants (rs1048661, rs3825942, and rs2165241) were determined in 68 consecutive Japanese patients with CRVO [15 with exfoliation syndrome (EX+) and 53 without exfoliation syndrome (EX−)] and 90 control patients with cataract without EX (CT).The frequencies of the rs1048661 and rs3825942 variants showed borderline difference between the CRVO and CT groups (p = 0.04085 and p = 0.06088, respectively, for allelic frequencies, and p = 0.06838 and p = 0.03482, respectively, for genotypic frequencies). Compared with the CT group, subgroup analysis showed that the CRVO EX+ group had significant differences in the allelic and genotypic frequencies of rs1048661 (p = 0.0006447 and p = 0.0001392, respectively) and had borderline differences in the allelic and genotypic frequencies of rs3825942 (p = 0.03403 and p = 0.07341, respectively), while the CRVO EX− group did not (p = 0.1324–0.6306). Subgroup analysis showed that the frequencies of rs2165241 did not differ between the CRVO and CT groups.When theLOXL1variants were used as disease markers for clinically undetectable EX, there was no association between CRVO and EX. The results suggested that theLOXL1variants, which are well-established markers for EX, are not likely genetic markers for CRVO in Japanese subjects.