With the advent of transcriptome profiling techniques, an enormous amount of data has been generated in the field of molecular nephrology. We will review analysis tools and challenges for genomic approaches and present their application in gene-expression studies on kidney biopsies. The findings in this rapidly evolving field may ultimately complement histopathological analysis, the current diagnostic and prognostic gold standard. Altogether, genomics may bring nephrology one-step closer to a systematic understanding of biological processes involved in renal disease.