Epstein–Barr virus (EBV) plays an etiological role in various diseases. EBV-associated lymphoproliferative disorder (LPD) is usually observed in individuals with congenital or acquired immune deficiencies but was also recently reported in non-immunocompromised individuals. Two cases of immunocompetent patients with EBV-associated T-cell LPD of the small bowel and colon who were initially misdiagnosed as Crohn's disease (CD) are reported here. EBV-associated T-cell LPD with primary gastrointestinal tract involvement can manifest as multiple discrete ulcers of the small and/or large bowel that are similar to the lesions found in CD or intestinal tuberculosis. However, when patients have multiple intestinal ulcers that are not typical of CD or intestinal tuberculosis and the clinical course is unusual, clinicians should consider the possibility of EBV-associated LPD that involves the gastrointestinal tract because the treatment strategy and prognosis are completely different.