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Amblyopia (lazy eye) is a neurodevelopmental disorder of vision with no ocular pathology. The loss of vision in the amblyopic eye is assumed to be the main deficit in amblyopia, which has resulted in visual acuity (VA) being the primary outcome measure for treatment. Here we used a binocular orientation combination task to quantitatively assess the binocular status by measuring the binocular balance. We set out to determine whether amblyopes who reach the acuity-based end point have a residual binocular imbalance. Our results suggest that even amblyopes who have regained normal acuity have residual binocular deficits over a wide range of spatial frequencies. A further control study suggests that these binocular deficits could not be explained by any residual contrast sensitivity deficits of the amblyopic eye. Consequently, amblyopia is not the primary problem and VA is not the appropriate end point measure.