Cytomegalovirus (CMV) infection of the GI tract is a common problem in patients immunosuppressed by HIV or organ transplantation. The esophagus and colon are the most common sites of involvement. Recent developments in diagnosis, such as immunohistochemical staining, shell vial assay and PCR, aid in early detection and predicting the prognosis of CMV disease in susceptible individuals. Although current drugs have limitations in terms of toxicity, drug interactions and resistance, newer drugs appear promising.