The aim of the study was to examine the severity of clinical symptoms of acute cystitis and the level bacteriuria in female patients who underwent to laparoscopic surgery followed by a postoperative administration of dienogest 2 mg and combined oral contraceptives pills (COCP). One hundred and forty five women who had a laparoscopic surgery prospectively were enrolled. Criteria inclusions were the age from 30 to 45 years old; body mass index (BMI) absence of previous hormonal therapy at least 6 month and recent performed a laparoscopy surgery for endometriosis. The women (n = 35) who had uterine myoma, abnormal coagulation profile; concomitant neoplastic diseases; chronic pelvic inflammatory disease and chronic recurrent cystitis were excluded from study. The female patients were assigned into both groups treatment: group I (n = 54) and group II (control, n = 56) who received dienogest 2 mg once daily and COCP, respectively. During follow-up three female patients of group I were withdrawn due to prolonged genital bleedings. The final analysis included 105 women. The patients of both groups had a low level of bacteriuria <103 CFU/ml without clinical symptoms of acute cystitis before treatment. The level of bacteriuria in-group I significantly increased from 102 to 106 CFU/ml whereas in-group II did not exceed 102 CFU/ml during 4 weeks of hormonal treatment. The differences of values of acute cystitis symptom score (ACSS) for differential, typical, quality of life domains were statistically significant after 4, 8 and 12 weeks of therapy in-group I compared with group II. During 3 months of hormonal treatment with dienogest 2 mg in group I, the acute cystitis developed in 10 (18.5%), in 19 (38%) and in 34 (68%) women at 4, 8 and 12 weeks of follow-up, respectively. All cases of acute cystitis in-group I were successfully treated with fosfomycin trometamol 3 g single dose or nitrofurantoin 50 mg four times a day during 5 days. We concluded that the dienogest might increase the level bacteriuria and severity of clinical symptoms of acute cystitis during a postoperative prophylaxis of endometriosis. Impact statement What is already known on this subject? Dienogest is a 19-nortestosterone derivative progestogen that is highly selective for progesterone receptors with high efficacy for reducing endometriosis-related pelvic pain syndrome. The administration of dienogest is a standard treatment option after laparoscopic excision of endometrial heterotopic tissue with prophylactic purpose. However, there are some adverse events, which are a cause for discontinuation. What do the results of this study add? Despite the low incidence of urinary tract infection (1–5.4%) reported in different studies this study has shown that there was a significant increase of level bacteriuria and severity of clinical symptoms of cystitis in the dienogest group. What are the implications of these findings for clinical practice and/or further research? The implications of these findings are that the administration of dienogest may lead to enhancing of clinical symptoms of cystitis and increasing bacteriuria in some women after operative treatment of endometriosis.