OBJECTIVE: Reasons why some persons with spinal cord injury (SCI) experience recurrent urinary tract infections more than others are poorly understood. We performed a prospective study of bacterial flora of the urethra and perineum in men with and without bacteriuria to understand more completely the relationship between bacterial colonization and invasion of the urinary tract. METHODS: Urine, urethra, and perineum cultures were obtained from 70 men. Microbial flora of these sites was compared for men with and without bacteriuria. RESULTS: Urine colony count was 0 in 16 (22.9%) men. Perinea in 2 men (12.5%) and urethras in 6 men (37.5%) were colonized with various gram-negative bacilli, enterococci, and/or Staphylococcus aureus. Among 54 (77.1%) men with bacteriuria, uropathogens were shown in the perineum in 31 (57.4%) and in the urethra in 46 (85.2%). In 40 (74.1%) of men with bacteriuria, at least one bacterial species present in the urine was also found in the urethra and/or perineum. Differences in the occurrence of uropathogens in men with and without bacteriuria were statistically significant, and organisms were present in higher numbers in men with bacteriuria. CONCLUSION: Men with SCI who have bacteriuria are significantly more likely to be colonized in the distal urethra and perineum with uropathogens that are often present in the urine in comparison with men without bacteriuria.