A prospective study. To investigate the risk factors predicting upper urinary tract (UUT) deterioration in patients with spinal cord injury (SCI). Beijing, China. We reviewed the medical records and UUT imaging studies of 112 patients, with a mean follow-up of 2 years. Variables evaluated for possible influence on UUTs included patient age, gender and educational background; injury level and completeness; bladder management method; and the presence of adverse outcomes such as recurrent urinary tract infections and bladder stones. Video urodynamic data were also reviewed. Total renal function was assessed by serum creatinine. UUT abnormalities were assessed by renal ultrasound or magnetic resonance imaging. Lumbosacral spinal cord lesions likely contribute to UUT deterioration. UUT abnormalities were present in 23 patients (65.7%) in a spontaneous voiding group, 10 patients (20%) in a clean intermittent catheterization group, 15 patients (78.9%) in an indwelling urethral catheterization group and 7 patients (87.5%) in a suprapubic Foley catheterization group (P<0.001). When dividing bladder management method into two groups, catheter-free (spontaneous and intermittent voiding) and indwelling catheter (urethral and suprapubic catheterization), there was UUT dysfunction in 33 patients (38.3%) and 22 patients (81.5%), respectively (P<0.001). Lumbosacral SCI and chronic indwelling urethral and suprapubic catheterization were predictors of UUT deterioration.