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Purpose: This study aimed to evaluate the clinical course and prognostic factors of acquired third, fourth, and sixth cranial nerve (CN) palsy grouped according to etiology. Methods: This study involved a retrospective review of the medical records of 153 patients who were diagnosed with acquired paralytic strabismus from January 2004 to July 2015. Outcomes, recovery rates, and time to recovery were investigated according to the affected CN: CN3, CN4, and CN6 palsies. The patients were classified into four groups based on etiology: idiopathic, traumatic, neoplastic, and vascular. Results: The mean age of the patients was 59.8 ± 14.5 years and the mean follow-up period was 10.8 months. Out of the 153 patients, 63 (41.2%) had CN3 palsy, 35 (22.9%) had CN4 palsy, and 55 (35.9%) had CN6 palsy. The most common causes were vascular related (54.9%), followed by idiopathic (28.1%), trauma (8.5%), and neoplasm (5.88%). About 50% of the patients recovered within six months. Among the four etiologic groups, the idiopathic group showed the best prognosis because about 50% of the patients in this group recovered within three months. This was followed by the vascular, traumatic, and neoplastic groups. Cox proportional hazard analysis revealed a significant association between the baseline prism diopter and recovery rate. Conclusions: The prognosis and natural history of paralytic strabismus vary depending on its cause. The vascular group had the best recovery rate and shortest recovery time, whereas the neoplastic group required the longest time to recover.