It has long been known that a number of diseases affecting the kidney are the result of genetic defects passed on through the generations. Whereas some of these defects are rare, others, eg, the cystic diseases, are among the most common. Our understanding of the underlying pathobiology in these disorders based on physiologic and cell biologic studies is variable—we suspect that the V2 vasopressin receptor is defective in nephrogenic diabetes insipidus; we know that the glomerular basement membrane in Alport syndrome is abnormal; we suspect that a tumor suppressor gene is defective in Wilms tumor; and we lack a unifying hypothesis regarding cystic degeneration of the kidney. The advent and rapid progress of molecular biology have permitted an entirely new approach to understanding these diseases, allowing the expected identification of mutations in the V2 receptor, the unexpected finding that a novel collagen gene is responsible for many Alport syndrome cases, and the somewhat less-unexpected finding that only one of several genes responsible for renal cancers has been identified. Further, we are beginning to unravel the complex pathways responsible for cystic changes in the kidney. This review integrates these molecular biologic discoveries with the known pathobiology of disease to achieve a more complete understanding of the whole process.