AIM: To analyze and screen the methylation status of whole-genome in age-related cataract samples. METHODS: Anterior lens capsule samples were collected from age-related cortical cataract patients over 50 years of age with LOCS III score of nuclear color ≥4 along with control subjects. DNAs were extracted and subjected to methylation microarray for the identification of methylated genes employing the high-throughput sequencing approach. RESULTS: Compared with the control group, 843 sites were found methylated, including 802 hypermethylation sites with 542 corresponding genes, 41 demethylation sites with 29 corresponding sites. COL4A1, GJA3, SIPA1L3 were confirmed by mass spectrometry, the results were consistent with high-throughput sequencing. CONCLUSION: DNA methylation microarrays is an efficient way for screening the aberrantly methylated genes. In this study, we are able to screen a few age-related cataract genes such as COL4A1, GJA3, and SIPA1L3 for their aberrant methylation patterns in cataract patients however further work is warranted to understand the significance of these findings.