Cytomegalovirus (CMV) infection is a common human viral infection, affecting 40% to 100% of normal adult, especially in the immune compromised patients. CMV infection can produce variable gastrointestinal (GI) diseases in healthy adults, but can cause severe life-threatening illness involving many organs, including lung, retina, central nervous system, liver and GI tract in immunocompromised host. We experienced CMV colitis with colon perforation in a SLE patient during low dose steroid and azathioprine therapy, and she recovered after medical treatment without surgical interventions. A 33-year-old woman was diagnosed as SLE 7 years ago and treated with low dose, immunosuppressive therapy during 6 years. She complained of a severe abdominal pain and hematochezia. She was diagnosed as CMV colitis with colon perforation by pathologic, immunologic and image studies. After medical treatment, such as intravascular ganciclovir, there was progressive medical improvement, but has been a recurrent CMV colitis with lower GI bleeding.