Abstract Background Approximately 25% of hospitalized patients have a urinary catheter, and catheter associated urinary tract infection is the most common nosocomial infection in the US, causing >1 million cases/year. However, the natural history of the biofilms that rapidly form on urinary catheters and lead to infection is not well described. Findings We characterized the dynamics of catheter colonization among catheters collected from 3 women and 5 men in a trauma burn unit with different indwelling times using TRFLP and culture. All patients received antibiotic therapy. Results: Colony-forming units increased along the extraluminal catheter surface from the catheter balloon to the urethra, but no trend was apparent for the intraluminal surface. This suggests extraluminal bacteria come from periurethral communities while intraluminal bacteria are introduced via the catheter or already inhabit the urine/bladder. Richness of operational taxonomic units (OTUs) increased over time on the intraluminal surface, but was constant extraluminally. Conclusions OTU community composition was explained best by time rather than axial location or surface. Our results suggest that catheter colonization can be very dynamic, and possibly have a predictable succession.