The aim of this study was to compare the thickness of the retinal nerve fiber layer (RNFL) and fovea of strabismus cases with normal cases and assess the effect of amblyopia on the results. The partipicians were divided into four groups. Group 1 included both eyes (40 eyes) of strabismus patients without amblyopia. Patients eyes, who had stabismic amblyopia, divided in two group as amblyopic eyes (21 eyes in Group 2) and the other eyes (21 eyes in Group 3). Group 4 enclosed both eyes (40 eyes) of the controls. The thickness of the RNFL across the superior quadrant in Group 1 was thinner with respect to that of the control group (Group 4) (p< 0.05). The mean thickness of the RNFL across the superior and inferior quadrants in Group 2 and Group 3 was thinner in comparison to Group 4 (p< 0.05). Moreover, the macular thickness in the nasal quadrant was thicker in Group 3 than Group 1 (p= 0.041). The macular thickness in the inferior quadrant was thicker in Group 2 than Group 1 (p= 0.043). The thickness of the fovea center and macular temporal quadrant in Group 3 was thicker than Group 4 (p= 0.04, p= 0.005, respectively). In this study, that was observed the structural changes in the retina of the strabismus patients with and without amblyopia. These retinal alterations may be result of structural changes in lateral geniculate body in cases with amblyopia which has been reported in previous studies. Larger case series are needed to clarify this hypothesis.