Aim: To evaluate whether intestinal microbiota predicts the development of new-onset urinary tract infections (UTIs) in postmenopausal women with prior recurrent UTIs (rUTIs). Patients & methods: Fecal samples (n = 40) originated from women with rUTI who received 12 months’ prophylaxis of either trimethoprim–sulfamethoxazole (TMP–SMX) or lactobacilli. Microbial composition was assessed by 16S rRNA pyrosequencing. Results: At baseline, fecal microbiota of women with zero and more than or equal to four UTIs during follow-up showed no significant differences. Only TMP–SMX prophylaxis resulted in reduced microbial diversity. Microbial structure of two samples from the same woman showed limited relatedness. Conclusion: In postmenopausal women with rUTI, the intestinal microbiota was not predictive for new-onset UTIs. Only TMP–SMX, and not lactobacilli, prophylaxis had effects on the microbial composition. Data in ENA:PRJEB13868.