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To evaluate the thickness of the macular ganglion cell and inner plexiform layer (GCIPL) using spectral domain optical coherence tomography (SD OCT) in patients with brain lesions.This case-control study included 58 healthy subjects and 98 patients with brain lesions confirmed by MRI. GCIPL and peripapillary retinal nerve fiber layer (pRNFL) thicknesses were determined using the Cirrus SD OCT. Area under the receiver operating characteristic curve (AUC) values of pRNFL and GCIPL thickness were used to discriminate patients with brain lesions from normal controls.Average GCIPL thickness showed a good correlation with visual field mean deviation (r2=0.342, p<0.001). All GCIPL parameters, including average thickness (71.9±8.6 vs 85.1±4.8 μm, p<0.001), differed between the patient and control groups. The AUC of the average GCIPL thickness was significantly greater than that of average pRNFL thickness (0.941 vs 0.823, p<0.001).Our results suggest that various kinds of brain lesions with different locations show considerable reduction in GCIPL thickness. Thickness of the GCIPL performed better than conventional pRNFL thickness for the diagnosis of retinal ganglion cell damage induced by brains lesions. The pattern of GCIPL loss may be of particular usefulness in recognising a potential intracranial lesion in cases suspected of having normal-tension glaucoma. GCIPL thickness determined by OCT can be an early and useful marker to estimate the status of the visual pathway in various brain lesions.