Purpose: To assess macular choroidal thickness (CT) and axial length measurements in children with anisometropic amblyopia and to compare the measurements with that of fellow non-amblyopic eyes and age-sex matched controls. Methods: Forty patients with anisometropic amblyopia and 40 age-/sex-matched controls were evaluated in this study. Eyes were classified into three groups as follows: amblyopic eyes (n=40), fellow non-amblyopic eyes, and healthy eyes (n=40). All subjects underwent complete ophthalmic examination and macular choroidal thickness measurements by enhanced depth imaging method of the Spectralis optical coherence tomography system. CT was measured at the fovea and at 1000-m intervals from the foveal center in both temporal and nasal directions. The statistical assessment was performed with the assistance of one-way analysis of variance (ANOVA) and Pearson's correlation test. Results: The mean subfoveal CT was 389.35, 349.07, and 315.8m in the amblyopic, fellow non-amblyopic and healthy eyes, respectively. Choroid was thickest in subfoveal and thinnest in nasal regions among all groups. Both amblyopic and fellow non-amblopic eyes were more hyperopic than healthy eyes. While the subfoveal and nasal CT in amblyopic eyes and fellow eyes were significantly higher than healthy eyes, the temporal CT in amblyopic eyes was significantly higher than in healthy eyes. There was a significant positive correlation between the CT of the subfoveal, nasal, and temporal regions and the refractive state (r=0.432 p=0.001; r=0.324 p=0.001; r=0.215 p=0.01, respectively). Conclusion: The macular choroidal thicknessnot only in amblyopic eyes but also in non-amblyopic fellow eyeswas significantly thicker than in the healthy subjects. The thick choroid in amblyopic and non-amblyopic fellow eyes may indicate bilateral delay of emmetropization, which probably means amblyopia affecting the visual feedback of both eyes.