The completion of the Human Genome Project (HGP) in 2003 has laid the foundation and driven the technological advancements necessary for the study of the genetics of complex, multi-factorial diseases, such as those affecting the kidney. The International HapMap Project has built upon the HGP through the systematic identification and cataloguing of genetic variation across human populations. Translating the mass of data generated by these studies into useful clinical knowledge is now a major undertaking in nearly all areas of medicine, including the field of Pediatric Nephrology. Much of this work will revolve around linking particular patient phenotypes to genomic and proteomic data, such as genotype, expression profile, and protein biomarkers. As evidenced by the etiological advances made in various kidney disorders resulting from the application of genome-wide linkage analyses in the 1990’s, there are a number of unique aspects of Pediatric Nephrology that make it an area particularly suitable to genomic exploration with such novel technologies as genome-wide association and expression analyses. These aspects relate both to the clinical characteristics, as well as to public health and epidemiological concerns, of pediatric kidney diseases.