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Diarrhea usually appears early following autologous hematopoietic stem cell transplantation (ASCT) due to toxic mucosal damage and neutropenia. Infectious agents also cause diarrhea in the post-transplantation period, with Clostridium difficile (C. difficile) being most common. In contrast, cytomegalovirus (CMV) enterocolitis is extremely rare after ASCT. We report a case of a 55-year-old male who underwent ASCT for non-Hodgkin lymphoma that was complicated by severe persistent diarrhea resulting in significant hypovolemia and electrolyte imbalance. Prior to transplantation, the patient received rituximab in combination with chemotherapy (R-CHOP/R-DHAP) followed by a bendamustine-based conditioning regimen (BeEAM). After treatment with oral metronidazole, vancomycin and fidaxomicin, diarrhea persisted despite undetectable C. difficile toxin, with elevation of hepatic enzymes. Eventually, CMV infection was diagnosed by real-time polymerase chain reaction and treated with ganciclovir and valganciclovir. Due to hypogammaglobulinemia following previous rituximab treatment, CMV immunoglobulins were also administered. The patient's condition gradually improved with CMV DNA being undetectable in serum. This case shows that diarrhea may be caused by concurrent infection with C. difficile and CMV after ASCT. Bendamustine-induced colitis and prior rituximab treatment may have been additional risk factors in this patient. Therefore, more comprehensive workup of diarrhea is needed in ASCT recipients treated with these agents.