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Contrast sensitivity function (CSF) in amblyopes has been studied extensively, with few studies on amblyopia associated with myopic anisometropia. The purpose of this study was to investigate CSF of amblyopic eyes in children with myopic anisometropia compared to fellow eyes of the amblyopic children, as well as to control subjects with high myopia but no amblyopia.Twenty amblyopic children with myopic anisometropia (range of visual acuity in the amblyopic eye: 6/10 to 6/100) and 16 control subjects with high myopia (< −6.00 D) but no amblyopia were recruited. CSF with linear sine-wave gratings was assessed at 1.5, 3, 6, 12 and 18 cycles per degree (cpd) in the amblyopic, fellow and control myopic eyes. Multivariate analysis of variance was used to compare logCS of the amblyopic, fellow and control myopic eyes after adjusting for age and race.The average degree of myopia in the amblyopic eyes was −10.46 D (range: −5.00 to −18.25 D). The average degree of myopia in the right eyes of control subjects was −8.61 D (range: −6.25 to −13 D). A statistically significant difference was found in logCS among the three groups of eyes at all frequencies (p < 0.001) except at 1.5 cpd. CSF of amblyopic eyes was statistically significantly lower than that of control myopic eyes at 3, 6, 12 and 18 cpd but not at 1.5 cpd. No significant difference in logCS was found between control myopic and fellow eyes. The co-variates (age and race) were not significantly related to the logCS (p > 0.05). Reduced CSF of the amblyopic eyes at the middle frequencies was associated with the degree of anisometropia.CSF at the middle and higher frequencies was reduced in the amblyopic eyes associated with myopic anisometropia compared to the fellow eyes of the same amblyopic children as well as to eyes of control subjects with high myopia but no amblyopia.