Background: In genitourinary tuberculosis the diagnosis is usually delayed because of its non-specific presentation and variable radiographic appearance which often mimics other pathological lesions, with the consequence that a number of patients present with non-functioning kidneys, ureteral stricture and shrunken bladders. Aim & Objective of the study: The main of the present study is to evaluate the role of urinary PCR in the detection of mycobacterium tuberculosis in patients with a clinical suspicion of genitourinary tuberculosis and to compare its sensitivity with urine for AFB smear, urine for Mycobacterium tuberculosis culture and bladder biopsy. Materials and Methods: This is a prospective study of patients with a diagnosis of genitourinary tuberculosis who underwent treatment in Nizam's institute of medical sciences between September 2016 to December 2017. 60 patients with a diagnosis of genitourinary tuberculosis who underwent treatment were taken initially into the study. Results: In the present study: Urine for AFB staining was positive in 20(35.05%) patients, urine for MTB culture was positive in 28 (49.12%) patients. Urinary PCR to identify the mycobacterial DNA was positive in 16(61.40%) of 57 clinically suspected cases. The urinary PCR was falsely positive in none and falsely negative in 22(38.59%) patients. Results revealed that, kidney is involved in 26 cases and is the most common organ involved in our study along with Urethra (26 cases) and bladder (24 cases), urethra (8 cases). Epididymis was involved in 4 cases. Overall Radiological abnormalities suggestive of GUTB were found in 46(80.7%) cases. Overall GUTB was identified by direct identification of bacilli by Urine PCR/Urine for AFB STAIN/ urine for MTB Culture in 92.98% of the cases. It was identified by HPE also in 77.77%. Strong clinical and radiological suspicion with NO evidence of bacilli was present in 7.02% cases. Conclusion: The present study concluded that, the sensitivity of Urinary PCR is high (61.40%) when compared to the sensitivities of urine for AFB staining (35.08%), MTB culture (49.12%) and bladder biopsy (41.66%).