Highlights • In the patients with DPD deficiency, advert events appear more rapidly than usual and can be lethal. • Cytomegalovirus enterocolitis is likely to occur in the state of immunosuppression and lethal because of massive bleeding or perforation. • Screening for DPD deficiency should be done, and genetic study can be effective screening for DPD deficiency., Introduction 5-Fluorouracil (5-FU) is widely used for cancer treatment. The reduced activity of dihydropyrimidine dehydrogenase (DPD), the key enzyme in 5-FU inactivation, increases a patient’s risk of developing severe 5-FU related toxicity. However, screening for DPD deficiency is rarely performed before 5-FU administration. Presentation of case Our patient was a 69-year-old man with rectal cancer (T2N1bM0 stage IIIA) who underwent laparoscopic low anterior resection. He developed severe neutropenia and diarrhea 15 days after the administration of capecitabine for adjuvant chemotherapy, and was admitted to our hospital. Four days after admission, he was transferred to the intensive care unit for sepsis. DPD protein screening revealed DPD deficiency. On day 27, massive melena suddenly appeared. He died of continual bleeding 41 days after admission. Pathological autopsy revealed cytomegalovirus enterocolitis. Discussion The administration of 5-FU to patients with DPD deficiency is lethal. Genotypic and phenotypic assessments are reliable tests for DPD deficiency. A genetic study can effectively screen for DPD deficiency; however, its use has not been established in the national insurance system. Patients with DPD deficiency tend to develop severe neutropenia, so clinicians should pay attention to opportunistic infections such as cytomegalovirus enterocolitis. Conclusion Screening for DPD deficiency is necessary prior to 5-FU administration.