Isolated sphenoid sinus disease (ISSD) is a relatively uncommon disease. The present study is a retrospective review of 122 patients with ISSD who were treated at the Department of Otolaryngology, Eye, Ear, Nose and Throat Hospital at Shanghai Medical University over a 25-year period. The diagnosis of ISSD was made on the basis of history and physical examination, signs and symptoms, nasal endoscopy, and computed tomography (CT) and magnetic resonance imaging (MRI). The final diagnosis of ISSD was confirmed by histopathologic and microbiological examinations of the surgical specimens. The pathological findings in this study included sphenoid cyst (47 cases), sphenoid sinusitis (31 cases), fungal disease (19 cases), inverted papilloma (4 cases), sphenochoanal polyp (1 case), foreign body (8 cases), malignant tumors (8 cases), and others (4 cases). The most common initial symptom was headache, followed in decreasing order by visual changes, cranial nerve palsies, and nasal symptoms. The more frequent use of routine CT and MRI scanning, as well as endoscopy, in the diagnosis of sinus disease has led to an increase in the early diagnosis of ISSD. The recent advances in endoscopic sphenoidotomy has allowed for relatively safe and immediate treatment of ISSD, preventing late extension into adjacent vital structures, which is commonly fatal. Endoscopic surgery also enables the surgeon to make a precise pathological diagnosis.