The globally increasing number of patients with end-stage renal disease urges the identification of molecular pathways involved in renal pathophysiology, to serve as targets for intervention. Moreover, the identification of genetic risk factors or protective genes can aid tailored therapy. Tools that can be used to identify genes involved in renal disease include gene expression arrays, linkage analysis and association studies. Arrays are a powerful and widely used approach to the analysis of gene transcription and protein expression, whereas linkage analysis and association studies link disease susceptibility to particular genetic regions. Animal models are available to pinpoint the disease-associated genes. Candidate genes so far identified in renal disease include those encoding the podocyte proteins nephrin and podocin, the transcription factor WT1, the calcium channel TRPC6 and the enzyme phospholipase C-epsilon-1 (in congenital nephrotic syndrome and focal segmental glomerulosclerosis), and carnosinase (in diabetic nephropathy). In addition, linkage studies have identified chromosomal regions implicated in systemic lupus erythematosus, diabetic nephropathy and familial IgA nephropathy. Future studies will elucidate the emerging role of epigenetic regulation of gene expression in renal disease.