Kidney stone formation is a complex process, and numerous genes participate in this cascade. The binding and internalization of calcium oxalate monohydrate (COM) crystals, the most common crystal in renal stones by renal epithelial cells may be a critical step leading to kidney stone formation. Exposure to COM crystals alters the expression of various genes, but previous studies on gene expression have generally been limited. To obtain more detailed insight into gene expression, we examined gene expression profiles in renal epithelial cells exposed to COM crystals using cDNA macroarray. NRK-52E cells were exposed to COM crystals for 60 and 120 min. Poly (A)(+) RNA was isolated and converted into (32)P-labeled first-strand cDNA, then the cDNA probe was hybridized to the membrane. Hybridization images were scanned and the signal intensities were quantified. Expression of mRNA of 1,176 genes was analyzed with global sum normalization methods. Exposure to COM crystals altered the expression of some of the genes reported previously. Furthermore, novel genes were also identified. Over 20 genes were found to be regulated at least twofold. We performed a large-scale analysis of gene expression in renal epithelial cells exposed to COM crystals, and identified the genes differentially regulated. cDNA macroarray is a useful tool for evaluating gene expression in urolithiasis research.