The authors examined the effect of exotropia, esotropia, anisometropic amblyopia and hypermetropia on choroidal thickness in a prospective cross section study. The study included 100 patients and 20 controls with a mean age of 8.5±2.9 years; 61 female and 59 male. Choroidal thickness differed between amblyopic and fellow eyes significantly in anisometropic amblyopia but was not significantly different in other groups. Mean spherical equivalent refraction was significantly lower in control eyes compared to amblyopes, hypermetropes, anisometropic amblyopes and esotropes but not for exotropes. Visual acuity was significantly better in control eyes compared to esotropia, exotropia and anisometropic amblyopia eyes but not significantly different for hypermetropia and anisometropic fellow eyes. A positive correlation was found between spherical equivalent refraction and choroidal thickness with a negative correlation for visual acuity and choroidal thickness. The authors conclude that anisometropic amblyopia eyes have thicker choroids compared to controls and fellow eyes. However, esotropia and exotropia eyes do not have significant difference in choroidal thickness measures between eyes.