This study was performed to define the relation between colonization of genital skin flora and bacteriuria in spinal cord injured patients with neurogenic bladder dysfunction. Twenty-seven female and 23 male spinal cord injured patients were included in the study. Patients were evaluated regarding their type of bladder management, educational status, level and degree of the spinal cord lesion. Quantitative cultures were obtained from the perineum, labium/dorsum of penis, external meatus of urethra, and urine. We investigated whether the organisms isolated from urine were also present in one or more skin sites in every patient. In total 54 identical bacterial isolates were observed both from urine and one or more skin sites in 43 of the patients. Escherichia coli, Proteus mirabilis, Klebsiella pneumoniae, and Proteus stuartii were the most common bacterial isolates. The distribution of identical colonization of genital skin flora with urine were as follows: 30 in urethra, one in perineum, four in urethra and perineum, nine in urethra and labium/dorsum of penis, and 10 in both three skin sites. Identical colonization of both perineum and labium/dorsum of penis with urine were significantly higher in female patients than those of males (P = 0.037, P = 0.003, respectively). No significant difference was found in the presence/distribution of colonization with respect to type of bladder management, educational status, and neurologic status. These results demonstrate the importance of the urethra, perineum, and labium/dorsum of penis as a source of bacteria causing urinary infection in spinal cord injured patients.