Background Uncomplicated urinary tract infections (UTIs) in women are usually managed in primary care with antibiotics. However, many women seem to prefer to handle UTI symptoms with nonsteroidal anti-inflammatory drugs (NSAIDs) and other remedies. The aim of this study was to compare UTI management as recommended by physicians with the patients’ management at home.Methods This prospective cohort study in German primary care is based on clinical data from local practices and patient questionnaires. Participating women completed a baseline data sheet in the practice; their urine sample was tested by a dipstick in the practice and cultured by a laboratory. The women reported treatment and symptom-related impairment on an eight-item symptom questionnaire daily for 7 days. Using growth curve models, we analysed the influence of time on the total severity score to examine how symptoms changed across days. We then examined whether symptom severity and symptom course differed between patients who took antibiotics or NSAIDs.Results A total of 120 women (mean age of 43.3 ± 16.6 years) were enrolled. The urine dipstick was positive for leucocytes in 92%, erythrocytes in 87%, and nitrites in 23%. Physicians prescribed antibiotics for 102 (87%) women and recommended NSAIDs in 14 cases. According to the women’s reports, only 60% (72/120) took antibiotics, while the remainder took NSAIDs and other remedies. Symptoms declined from day 0 to day 6, irrespective of whether women decided to take an antibiotic, NSAIDs, none or both, as confirmed by a significant curvilinear time effect (B = 0.06, SE = 0.005, p < .001). The symptom course, however, was moderated by taking antibiotics so that the change in symptom severity was somewhat more pronounced in women taking antibiotics (B = 0.06) than in the remainder (B = 0.04).Conclusion A substantial proportion of women did not follow their physicians’ treatment recommendations, and many used NSAIDs. All women had a good chance of recovery irrespective of whether they decided to take antibiotics. A sensitive listening to patient preferences in the consultation may encourage physicians to recommend and prescribe symptomatic treatment with NSAID more often than antibiotic medicines.