Huntington's disease is a neurodegenerative disorder with an autosomal dominant inheritance pattern. Patients with Huntington's disease show an increased risk of aspiration pneumonia when the pharyngeal muscle is invaded. We report a case of advanced-stage Huntington's disease in which the patient received right middle lobectomy for a lung abscess caused by repeated aspiration. The best lung isolation technique has not yet been established in these patients. We successfully performed selective lobar isolation of the right lower and middle lobes using a double lumen tube and a Fogarty embolectomy catheter.