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Amblyopia is a cerebral visual impairment considered to derive from abnormal visual experience (e.g., strabismus, anisometropia). Amblyopia, first considered as a monocular disorder, is now often seen as a primarily binocular disorder resulting in more and more studies examining the binocular deficits in the patients. The neural mechanisms of amblyopia are not completely understood even though they have been investigated with electrophysiological recordings in animal models and more recently with neuroimaging techniques in humans. In this review, we summarize the current knowledge about the brain regions that underlie the visual deficits associated with amblyopia with a focus on binocular vision using functional magnetic resonance imaging.The first studies focused on abnormal responses in the primary and secondary visual areas whereas recent evidence shows that there are also deficits at higher levels of the visual pathways within the parieto-occipital and temporal cortices. These higher level areas are part of the cortical network involved in 3D vision from binocular cues. Therefore, reduced responses in these areas could be related to the impaired binocular vision in amblyopic patients. Promising new binocular treatments might at least partially correct the activation in these areas. Future neuroimagin