The process of nephrolithiasis development is poorly understood at the molecular level. Here, we constructed a cDNA microarray from a rat kidney normalized cDNA library, and investigated the pattern of gene expression in rat kidneys from a calcium oxalate (CaOx) nephrolithiasis model. One hundred and seventy-three genes were found to be at least 2-fold regulated at one or more time points during progression of nephrolithiasis. RT-PCR and immunohistochemical analyses confirmed differential expression at both transcriptional and translational levels of genes identified by cDNA microarray screening. The differentially regulated genes were grouped into six clusters based on their expression profiles; the magnitude and the temporal patterns of gene expression identified known and novel molecular components involved in inflammation and matrix expansion in the CaOx nephrolithiasis kidney. This microarray study is the first report on gene expression programs underlying the process of nephrolithiasis.