OBJECTIVE Concerns exist about deleterious renal effects of low-carbohydrate high-protein weight loss diets. This issue was addressed in a secondary analysis of a parallel randomized, controlled long-term trial. METHODS Between 2003 and 2007, 307 obese adults without serious medical illnesses at three United States academic centers were randomly assigned to a low-carbohydrate high-protein or a low-fat weight-loss diet for 24 months. Main outcomes included renal filtration (GFR) indices (serum creatinine, cystatin C, creatinine clearance); 24-hour urinary volume; albumin; calcium excretion; and serum solutes at 3, 12, and 24 months. RESULTS Compared with the low-fat diet, low-carbohydrate high-protein consumption was associated with minor reductions in serum creatinine (relative difference, -4.2%) and cystatin C (-8.4%) at 3 months and relative increases in creatinine clearance at 3 (15.8 ml/min) and 12 (20.8 ml/min) months; serum urea at 3 (14.4%), 12 (9.0%), and 24 (8.2%) months; and 24-hour urinary volume at 12 (438 ml) and 24 (268 ml) months. Urinary calcium excretion increased at 3 (36.1%) and 12 (35.7%) months without changes in bone density or clinical presentations of new kidney stones. CONCLUSIONS In healthy obese individuals, a low-carbohydrate high-protein weight-loss diet over 2 years was not associated with noticeably harmful effects on GFR, albuminuria, or fluid and electrolyte balance compared with a low-fat diet. Further follow-up is needed to determine even longer-term effects on kidney function.