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Background The Infectious Diseases Society of America guidelines recommend either 14 days of trimethoprim-sulfamethoxazole (TMP-SMX) or 7 days of ciprofloxacin for the treatment of pyelonephritis. Antibiotic courses of 7 days of TMP-SMX vs 7 days of ciprofloxacin for pyelonephritis have not been previously compared. We evaluated the odds of a subsequent, symptomatic urinary tract infection (UTI) for women with Escherichia coli pyelonephritis receiving a 7-day course of TMP-SMX vs a 7-day course of ciprofloxacin. Methods Women ages 16 years and older with E. coli pyelonephritis presenting to 5 health care facilities in the greater Maryland area between 2010 and 2016 receiving either TMP-SMX or ciprofloxacin were included. Patients were excluded if they met any of the following criteria: (a) pregnancy, (b) dialysis dependency, (c) E. coli not susceptible to the treatment prescribed, (d) polymicrobial urine culture, or (e) >48 hours of antibiotic therapy other than TMP-SMX or ciprofloxacin. Results Of 272 women meeting eligibility criteria, 81 (30%) and 191 (70%) received 7 days of TMP-SMX and 7 days of ciprofloxacin, respectively. In an adjusted model, the likelihood of a recurrent UTI within 30 days for the TMP-SMX and ciprofloxacin groups was similar (adjusted odds ratio 2.30; 95% confidence interval, 0.72-7.42). Conclusions Our findings suggest that 7 days of TMP-SMX therapy may result in similar clinical outcomes compared with 7 days of ciprofloxacin for the treatment of pyelonephritis. Considering the frequency of pyelonephritis and risks of antibiotic resistance and associated toxicities, decreasing the duration of antibiotic therapy for pyelonephritis may impact a large number of women.