Background: D-Serine, a long-term undetected enantiomer of serine, is a biomarker that reflects kidney function and disease activity. The physiological functions of D-serine have been unclear. Methods: Dynamics of D-serine was assessed by measuring D-serine in human samples of living kidney donors using two-dimensional high-performance liquid chromatography, and by auto-radiographic studies in mice. Effects of D-serine on kidney were examined by gene expression profiling and metabolic studies using unilateral nephrectomy mice, and genetically modified cells. Results: Unilateral nephrectomy in human living kidney donors decreases urinary excretion and thus increases the blood level of D-serine. D-Serine is quickly and dominantly distributed to the kidney upon injection in mice, suggesting that the kidney is a main target organ. Treatment of D-serine at low dose promotes the enlargement of remnant kidney in mouse model. Mechanistically, D-serine activates the cell cycle for tissue remodeling through an mTOR-related pathway. Conclusions: D-Serine is a physiological molecule that promotes kidney remodeling. Besides its function as a biomarker, D-serine has a physiological activity that influences kidney function.