Specimens were examined from 70 female presenting with urinary tract infection. 50 patients were randomly treated with 7 days amoxicillin or bacampicillin and another 20 randomly received amoxicillin or enoxacin. Effective clearance of the infections was achieved with each antibiotic, and only minor side effects occurred. Bacteriological analyses of the urogenital flora demonstrated a relationship between urethral carriage and bladder infection, with Escherichia coli being the most common pathogen. Antibiotic resistant E. coli were isolated more frequently from the bladder, urethra, introitus and rectum following amoxicillin treatment compared to bacampicillin and enoxacin. An examination of the urogenital flora post therapy showed that an indigenous lactobacillus population had not been restored in the majority of patients. Rather, uropathogenic bacteria were found to dominate the urethra and introitus. The effects of antibiotics on urogenital flora is clearly a matter of importance. Future clinical trials should address this. It may be that artificial supplementation of indigenous bacteria is necessary to restore the flora back to normality.