Background A 63-year-old man with a 4-year history of Wegener's granulomatosis presented with hemoptysis, palatal ulceration and sensorimotor polyneuropathy. Investigations Physical examination, serologic testing, proteinase 3 enzyme-linked immunosorbent assay, IgG and IgM specific to Epstein-Barr virus enzyme-linked immunosorbent assay, MRI of the middle face, an ear, nose and throat consultation, immunohistochemical staining of an esophageal sample obtained from esophagogastroduodenoscopy, polymerase chain reaction of cytomegalovirus (CMV) DNA from esophageal and blood samples, and measurement of pp65 early antigen. Diagnosis Wegener's granulomatosis with progressive palatal ulceration and osseous destruction complicated by CMV-related esophagitis during induction treatment. Management Induction treatment with cyclophosphamide pulse therapy was discontinued and antiviral therapy with ganciclovir was started. Cyclophosphamide pulse therapy was later reintroduced, but there was subsequent CMV reactivation, and, therefore, cyclophosphamide pulse therapy was suspended again and ganciclovir and intravenous immunoglobulin were started. After control of CMV, cyclophosphamide pulse therapy was reinitiated. Prolonged immunosuppressive therapy controlled disease activity, without CMV reactivation.