The aim of our study was to examine the effect of hypermetropia and anisometropic, exotropic, and esotropic amblyopia on choroidal thickness. A prospective, cross-sectional, comparative study of 120 children under the age of 16 years was conducted. Choroidal thickness was measured in patients with hypermetropia, anisometropia, esotropia, exotropia, and controls. The mean subfoveal choroidal thickness in the control and hypermetropia groups was 323.9±69.0 µm and 348.9±64.5 µm, respectively. Mean choroidal thickness in amblyopic and fellow eyes was 387.4 and 351.9 µm in anisometropic, 353.8 and 338.7 µm in exotropic, 347.5 and 336.5 µm in esotropic, and 389.3 and 359.3 µm in esotropic+anisometropic groups, respectively. Choroid was significantly thicker in amblyopic eyes of anisometropic group compared to fellow (P=0.004) and control (P=0.03) eyes. The difference of choroidal thickness was not significant between both eyes and when compared to control eyes in the other groups. Anisometropic amblyopic eyes had thicker choroids compared to controls and fellow eyes. However the choroidal thickness was not significantly different between amblyopic and fellow eyes of esotropic or exotropic patients.