BACKGROUND Gastrointestinal involvement by cytomegalovirus (CMV) infection is a well recognised complication in patients taking steroid/immunosuppressive therapy or suffering from immunodeficiency and debilitating diseases. Rarely, CMV may affect immunocompetent healthy individuals. However, CMV infection presenting as isolated inflammatory polyps is unusual. METHODS We describe five patients (1 infant and 4 adults 56-80 years of age) with CMV-associated polyps that posed diagnostic difficulty. Four lesions were initially misdiagnosed as inflammatory fibroid polyp (n = 2), atypical/suspicious lymphoproliferative (n = 1) and mesenchymal (n = 1) lesion. RESULTS Underlying diseases were kidney transplantation (1), ulcerative colitis (1), and HIV infection (1). One elderly patient had pseudomembranous colitis but no significant co-morbidity. One patient had no relevant diseases. The lesions affected the colon (3), small intestine (1) and gastric antrum (1); one was multifocal. The size ranged from 0.3 cm to 2.0 cm. Histologically, all lesions showed extensive surface ulceration and abundant capillary-rich granulation tissue containing activated lymphoid cells, plasma cells, granulocytes, enlarged histiocytes and atypical fibroblasts. Eosinophils were prominent in two cases. Immunohistochemistry showed unequivocal intranuclear CMV inclusions. CONCLUSION These cases widen the spectrum of endoscopic and histological appearance of gastrointestinal CMV infection. Awareness of these unusual lesions should enhance detection and proper classification of this probably under-recognised CMV presentation.