Background and Purpose: Calculi from patients with musculoskeletal (MS) anomalies who are largely immobile and prone to urinary infections have been traditionally composed primarily of struvite and carbonate apatite. Because of substantial improvements in the care of these patients in recent decades, stone etiology may have shifted from infectious to metabolic. We assessed the composition of renal calculi and metabolic characteristics in a contemporary cohort of patients with MS anomalies who underwent percutaneous nephrolithotomy (PCNL). Patients and Methods: Retrospective analysis of patients who underwent PCNL between April 1999 and June 2009 and had follow-up 24-hour urine studies was performed. Patients with MS anomalies included spinal cord injury, myelomeningocele, muscular dystrophy, multiple sclerosis, cerebral palsy, or other clinical syndromes causing kyphoscoliosis and contractures. Results: Our cohort included 33 patients with MS anomalies and 334 consecutive patients as a control group who underwent PCNL and had metabolic workup. Stones were infectious in etiology in 18.4% and 6.2% in MS and control groups, respectively. Thus, most patients harbored stones of metabolic origin. Metabolic stones in the MS group were composed of 52.7% hydroxyapatite, 10.5% calcium oxalate, 7.9% brushite, 2.6% uric acid, 0% cystine, and 7.9% other. Metabolic stones in the control group were 50.5% calcium oxalate, 16.4% hydroxyapatite, 11.5% brushite, 10.8% uric acid, 4.3% cystine, and 0.3% other. Mean 24-hour urine values for patients with metabolic stones in MS/control groups were volume 2.18/1.87 L/d, pH 6.78/6.05, calcium to creatinine ratio 220/151 mg/g, and oxalate 44.8/39.5 mg/d. Conclusions: Although patients with MS anomalies are traditionally thought to harbor infection-related calculi, most will be found to have calculi of metabolic etiology. The incidence of calcium phosphate stones is high in this group of patients, perhaps reflecting their high urinary pH.