Kidney proximal tubules are composed of S1, S2, and S3 segments having different properties of excretion and substance reabsorption. Since renal toxicants such as cadmium and cisplatin cause segment-specific toxicity, it is important to examine the segment-specific transport and detoxification systems of renal toxicants. Here, we investigated the gene expression profiles of immortalized S1, S2, and S3 cells derived from each segment of mouse kidney proximal tubules. Microarray analyses showed distinct expression of various genes in each cell line. We compared the expression levels of selected genes related to the transport and detoxification of renal toxicants. Some genes showed segment-specific expression patterns similar to those observed in in vivo studies. The gene expression profiles of each cell line shown in this study will provide a foundation for the future utilization of immortalized S1, S2, and S3 cells for toxicity screenings as well as for the elucidation of renal toxicity mechanisms.