Extranodal natural killer (NK)/T-cell lymphoma, nasal type, is a rare type of non-Hodgkin's lymphoma with similar presentation to various benign inflammatory diseases. Adequate biopsy is required for a diagnosis because this lymphoma frequently coexists with large amount of necrosis and inflammation. In this study, a case of a 49-year-old woman presenting with a 3-week history of right maxillary alveolar ridge pain with a subsequent diagnosis of periodontitis is described. The patient's clinical condition deteriorated over a period of 6 weeks. Computed tomography delineated involvement of the right maxillary sinus, posterior part of the right pharynx and right nasal cavity. Immunohistopathology initially revealed Wegener's granulomatosis, followed by extranodal nasal-type NK/T-cell lymphoma. Severe refractory periodontitis in a background of Wegener's granulomatosis may be the initial presentation of extranodal NK/T-cell lymphoma, nasal type. In addition to careful examination, radiographic and laboratory testing, multiple large biopsies should be taken for immunohistochemical analysis to obtain an appropriate diagnosis.