We report a patient with a history of ulcerative colitis status after total proctocolectomy with an ileoanal J pouch who presented with marked, refractory pouchitis associated with a primary cytomegalovirus (CMV) infection. The patient had atypical lymphocytosis in the blood and serology consistent with primary CMV infection. Biopsies of the pouch revealed CMV inclusion bodies and yielded positive CMV cultures. The patient improved clinically with resolution of pouchitis after a 10-day course of therapy with gancyclovir and has remained in remission for over 5 yr. This is the first report of pouchitis associated with a primary CMV infection. This case demonstrates that CMV infection is in the differential diagnosis for causes of pouchitis, and it suggests that the pouch, like the colon, is a potential site for a primary CMV infection in an immunocompetent host.