Nephron number has emerged as a useful parameter for assessing the roles of specific genes and feto-maternal environmental factors in kidney development. Nephron number is also of clinical interest due to increasing evidence suggesting that low nephron number is associated with increased risk for developing chronic adult disease, including cardiovascular and renal disease. The physical disector/fractionator combination is considered the gold standard method for estimating total nephron number in kidneys. Here we describe the use of this method to estimate total nephron number in mouse and rat kidneys, and variations to the method required to estimate nephron number in larger species, including human.