We report a case of oral malodor associated with internal resorption. A 39-year-old male attended our hospital complaining of oral malodor. Utilizing organoleptic measurement, the halimeter test and gas chromatography, it was diagnosed as a strong halitosis caused by oral origin. The pocket probing depth of tooth 21 was 10 mm, and X-ray examination revealed a vertical bone loss around this tooth. The patient had received periodontal treatment at two dental offices previously, but the periodontal conditions and oral malodor persisted. We performed an initial periodontal preparation, however a deep pocket remained. We therefore performed a surgical inspection including flap reflection, and found that the tooth had a large perforating defect in the distal surface. The extracted tooth had multiple perforating defects covered with granulation tissues on all root surfaces including the root apex. Taking into consideration the anamnesis and X-ray examination of the extracted tooth, internal absorption was considered to have been the cause of the multiple perforating defects. After extraction of the causative tooth, oral malodor dramatically decreased. To our knowledge, this is the first report of an oral malodor associated with internal resorption.