a b s t r a c t Objectives: To evaluate the effect of the presence of pathogenic bacteria in urine on three bladder cancer genetic markers (Cytokeratin 19, Cytokeratin 20 and Uroplakin II mRNA), and to evaluate the reliability of each urine marker separately. Methods: Voided urine samples from 20 bladder cancer patients, 15 patients with urinary tract infection patients and 10 healthy volunteers were collected. Isolation and identification of bacteria was performed followed by determination of antimicrobial susceptibility of isolates. Evaluation of CK-19, CK-20 and UPII mRNA in urine by RT-PCR was carried out.Results: The most frequent organism isolated was Escherichia coli followed by Klebsiella pneumoniae. The overall sensitivity and specificity were 47.37% and 68.42%% for CK-19, 57.89% and 100% for CK-20 and 63.1% and 100%for UPII. Combined sensitivity and specificity of CK-20 and UPII biomarkers together was higher than that of each biomarker alone or even more than that of the three combined biomarkers. Conclusions: E. coli is the most predominant bacteria isolated from bladder cancer patients.Both CK-20 and UPII have different expression levels for both benign and malignant cases.Combined use of UPII and CK-20 may be a promising noninvasive tool for the detection of bladder cancer in urine for patients who have both symptoms of UTI and cancer.