John Cunningham virus (JCV) is a type of human polyomavirus.It s widespread virus detected in different population throughout the word. JCV encodes for T-Ag which have oncogenic capability through interaction with different regulatory pathways and can interfere with cell cycle control and genomic instability mechanisms. The association between JCV and colorectal carcinoma still awaits the final conformation. Determine the role of JCV in malignant transformation of colorectal carcinoma through the detection ofT-Ag gene and agnoprotein gene and demonstrating JCV DNA in both colorectal carcinoma tissue and normal colonic tissue biopsies. involved the use of 28 colonic tissue biopsies taken through colonoscopy from patients with colorectal cancer and 31 tissue biopsies from patients without CRC attended to GIT Endoscopic Unite of Oncology Hospital, Baghdad Teaching Hospital, and Al-Yarmouk Teaching Hospital during the period from June 2013 to march 2014. JCV T Ag and agnoprotein were detected by real time PCR and in situe hybridization, Viral DNA load of positive samples were determined by quantitative real-time PCR. out of 28 CRC cases, 16(57.1%) were positive for T-Ag compared to 9/33(27.3%) in non CRC patient (p=0.018), 12/28(42.9%) of CRC cases were positive for agnoprotein gene compared to 5/33(15.2%) in non CRC patient (p=0.016).While 15/28(53.6%) of CRC were positive JCV DNA by ISH compared to 10/33(31.3%) in non CRC patient(p=0.080). Significant differences between the study groups regarding glandular involvement (p=0.036) signals intensity(p=0.032), and pattern of involvement while no significant differences were found regarding stromal involvement (p=0.52). JCV exists in colorectal cancer tissue more than normal tissue and may play a role as an etiology for colonic carcinogenesis