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PURPOSE To examine the choroidal structure in children with anisometropic amblyopia using the binarization method. METHODS Thirty children with unilateral anisometropic amblyopia and 30 healthy age- and sex-matched controls were included in the study. Choroidal thickness was measured with optical coherence tomography. The choroidal layer was examined with the binarization method using ImageJ software (National Institutes of Health). The total choroidal area, stromal area, luminal area, luminal area to stromal area ratio, and choroidal vascular index were calculated. The values were compared by correlating the spherical equivalent (SE) (determined by an autorefractometer) with anterior chamber depth, axial length, central corneal thickness (measured by optical biometry), and choroidal thickness values. RESULTS Mean SE values were 3.75 ± 2.16 diopters (D) in the amblyopic eyes, 2.39 ± 2.09 D in the fellow eyes, and -0.27 ± 0.53 D in the control eyes. Best corrected visual acuity (BCVA) was 0.29 ± 0.11 logarithm of the minimum angle of resolution (logMAR) in the amblyopic eyes, 0.02 ± 0.04 logMAR in the fellow eyes, and 0 ± 0 logMAR in the control eyes. Choroidal thickness values were 351 ± 47 µm in the amblyopic eyes, 333 ± 55 µm in the fellow eyes, and 324 ± 51 µm in the control eyes. Luminal area to stromal area ratio values were 1.73 ± 0.13 in the amblyopic eyes, 1.76 ± 0.15 in the fellow eyes, and 2.02 ± 0.25 in the control eyes. Choroidal vascular index values were 63% ± 0.02 in the amblyopic eyes, 64% ± 0.02 in the fellow eyes, and 66% ± 0.03 in the control eyes. BCVA, SE, choroidal thickness, luminal area to stromal area ratio, and choroidal vascular index were significantly different in each group. The total choroidal area, luminal area, and stromal area were similar in all eyes. No correlation was found between choroidal vascular index and choroidal thickness, anterior chamber depth, axial length, and central corneal thickness. CONCLUSIONS In children with anisometropic amblyopia, the total choroidal area was relatively larger in both the amblyopic and the fellow eyes compared to the control eyes. Due to the higher stromal area and lower luminal area, both the amblyopic and the fellow eyes also had lower choroidal vascular index values than control eyes. [J Pediatr Ophthalmol Strabismus. 20XX;XX(X):XX-XX.].