Objectives: In this study we aimed to determine the incidence of BKV infection in patients undergoing chemotherapy for different types of cancer who present with cystitis. This study provides molecular evidence of a possible association between BKV and cystitis in cancer patient treated with chemotherapy. Materials and Methods: The study was performed on urine samples from 85 individuals (45 cancer patients during an episode of cystitis and compared with that detected in the urine of 20 cancer patients with no cystitis and 20 healthy individuals) in order to better evaluate the association of BK virus reactivation with cystitis. Detection of BKV in urine by real time PCR assay was done for all of the three groups. Results: Results on the detection of viral DNA from the urine samples demonstrated that 4 (8.89%) of cancer patients with cystitis, in 1 (5.00%) of cancer patients with no cystitis, while 3 (15.00%) of healthy controls, were positive. Recommendations:Our findings merit more studies to be done in a larger number of patients including multiple centers to help in establishing a causal association.