BACKGROUND A diagnosis and treatment of recurrent lower urinary tract infection (UTI) in women is still one of the unresolved problems of urology. The proper identification of the etiological factor determines the treatment tactics. Therefore, the most urgent issue of recurrent lower UTI is the differential diagnosis of the causative pathogens. METHODS A cytological study of urine was performed in 151 patients with recurrent lower UTI, who, according to the results of bacteriological and PCR studies of urine, were divided into three groups, depending on the etiological factor. The group 1 (n=70) included women with recurrent lower UTI of bacterial etiology, while in group 2 (n= 70) papillomavirus etiology was found, and in group 3 (n=11) candida species were the causative pathogens. The age of the patients ranged from 20 to 45 years (32.3+/-7.8). RESULTS In the majority of patients with recurrent lower UTI of bacterial etiology, the cytological features were represented by leukocytes, plasma, epithelial cells and bacteria in combination with actively phagocytic macrophages. In group 3, in addition to a large number of leukocytes (neutrophils) and epithelial cells, Candida mycelium was found. In group 2, signs of bacterial inflammation were minimal, while a predominance of lymphocytes, epithelial cells, and the presence of single neutrophils was seen. With papillomavirus lesions of the bladder, urothelial cell dystrophy with the presence of koilocytes developed. CONCLUSIONS A cytological examination of urine can confirm the etiology of the recurrent lower UTI and be an evidence-based criterion in the differential diagnosis of bacterial, candidiasis, and papillomavirus infection. Total transformation of the urothelium and vacuolization of urothelial cells, as well as an excess of lymphocytes in the urine in the absence of neutrophils, are the characteristic features of viral recurrent lower UTI.