OBJECTIVES: Vaginal estrogen therapy (VET) has been shown to decrease the risk of recurrent urinary tract infections (UTIs) in postmenopausal women, but the mechanism of action has not been fully described. Our objectives were to assess whether the postmenopausal urine inflammatory profile changes in response to VET. METHODS: We prospectively enrolled postmenopausal patients into 3 groups: (1) currently using VET without a history of recurrent UTIs (rUTIs); (2) history of UTIs, currently using VET; and (3) history of rUTIs, not using VET but willing to start. We followed patients over 6 to 19 months and collected urine samples at 3 time points. We performed comprehensive cytopathologic analysis, quantitative urine inflammatory scoring, and enzyme-linked immunosorbent assay for interleukin 6. RESULTS: Seventy patients were recruited (group 1, n = 30; group 2, n = 20; group 3, n = 20). Urine from patients in groups 2 and 3 demonstrated increased inflammatory cells, debris, and exfoliated urothelial cells. Quantitative urine inflammatory scores and interleukin 6 were significantly higher in postmenopausal patients with rUTIs not on VET (0.12 vs 0.93, P < 0.05) and decreased significantly after initiating VET (0.93 vs 0.38, P < 0.05). CONCLUSIONS: Postmenopausal women with rUTIs on VET demonstrate decreased cell shedding, reduced urine inflammatory scores, and decreased urine interleukin 6. Modulation of the genitourinary inflammatory profile may represent one mechanism through which VET helps prevent rUTIs in postmenopausal women.