Reduction in numbers of nephrons or decrease in kidney function due to a variety of diseases results in compensatory renal hypertrophy (CRH). Recently, it has been proposed that CRH may be a prerequisite for progression of renal injury; genetic dissection of CRH may be therefore helpful in understanding the process whereby people with partial renal insufficiency progress to end-stage renal disease. Since genetic analysis of CRH in humans is quite limited, we searched for genetic determinants of CRH after unilateral nephrectomy using a total genome scan of the mouse BXD recombinant inbred strains. We demonstrated that CRH is a highly heritable trait and we identified a quantitative trait locus on mouse chromosome 11 near the D11Mit14 marker that exerts a major effect on CRH (lod score = 3.4) and is responsible for approximately 52% of genetic variation in CRH. This marker maps near Ace, Gh, and Ngfr positional candidate genes.