Background/Aims Immunosuppressive therapy in ulcerative colitis (UC) may induce cytomegalovirus (CMV) infection or reactivation in the colonic mucosa and in turn exacerbate UC. However, it is unclear whether colonic inflammation itself affects CMV infection in UC. This prospective study evaluated the prevalence and clinical outcome of CMV infection in patients with new onset UC who have not been exposed to UC medication. Methodology A prospective, multi-center study was conducted in 65 patients with new onset UC. The presence of CMV was evaluated by a serology test and a histopathological examination including immunohistochemical staining. The assessment of clinical outcome was performed based on CMV positivity. Results Evidence of CMV infection was found in three (4.5%) patients with UC. Two patients with moderate disease activity improved with 5-aminosalicylate or steroid treatment. One patient with severe active colitis, however, required antiviral therapy. Conclusions CMV infection is rare in new onset UC, which suggests that use of immunosuppressive medications is an important risk factor for CMV infection in UC. However, CMV evaluation is necessary for severe active UC, even with new onset of the disease.