AIM: To identify the differences of gene expression between human age-related cataract and clear lenses. METHODS: The RNA were extracted from human age related cataract and clear lens epithelial cells, labeled with cy3/cy5 as probes, then were hybridized to cDNA chip containing 8 064 genes. The differential expressions of the genes were screened. Furthermore, a primary classification of these genes function was given. The expression levels of the identified genes were further evaluated by real time polymerase chain reaction. RESULTS: 286 genes expression were observed to increase and 438 genes expression were observed to decrease in cataractous lens epithelial cells as compared with normal lens. According to functional analysis, the changed genes in cataract lens are associated with lens structural components, cytoskeleton, cell cycle, apoptosis and stress responses. CONCLUSION: These data suggest that there are differences in gene expression between cataract and clear human lens epithelial cells. The majority of genes changed in cataract exhibited decreased expression. Processes associated with the down-regulated genes may reflect the inability of the lens to maintain its homeostasis and transparency.