Study design: Prospective analysis. Objectives: To investigate the colonization of the distal urethra and bladder during the initial stages of rehabilitation in acute spinal-cord injury (SCI) and to examine the association between bacteriuria and colonization of the distal urethra. Setting: Selcuk University Meram Faculty of Medicine, Konya, Turkey. Methods: A total of 27 patients with SCI (13 females and 14 males) and 40 controls without evidence of disease of the urinary tract were studied. Cultures were taken from the patients who applied clean intermittent catheterization and compared with normal subjects. Results: Escherichia coli was predominantly isolated from the urine and urethral cultures of both female and male SCI patients. Colonization of other bacteria in the urine and urethral cultures was similar in both female and male patients, except for Pseudomonas, which was colonized in male patients. In all, 72% of patients who had E. coli positive urethral cultures also had E. coli colonization in their simultaneous urine cultures. There was concordance between urethra and urine cultures concerning the growth of E. coli (P = 0.82). When urethral cultures collected 1 week before were evaluated in patients with E. coli positive urine cultures (n = 24 cultures), 15 of these urethral cultures also had E. coli colonization. There was concordance between urethra and urine cultures concerning the growth of E. coli (P = 0.66). Conclusions: Our study suggested that urethral flora was a significant source for the development of urinary infection in spinal cord-injured patients.