We present a case of late-onset ulcerative colitis (UC) complicated with cytomegalovirus (CMV) pneumonia revealed by autopsy. A 77-year-old woman had a diagnosis of UC, and received high-dose steroids and leukocytapheresis. Then she received ganciclovir because CMV-pp65 antigenemia test revealed positive which suggested systemic or colonic CMV infection. But ganciclovir was discontinued because of thrombocytopenia and liver dysfunction. After that she had interstitial pneumonia and died of a respiratory failure. Autopsy revealed CMV colitis based on UC, and CMV pneumonia with diffuse alveolar damage. Evaluation of CMV infection in patients with steroid-refractory UC should be considered before proceeding with immunosuppressive therapy or surgery, especially in elderly patients.