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To investigate the functional deficit of brain cortex in human ametropic amblyopia. Methods: The regional brain activation in ametropic amblyopia and healthy subjects evoked by visual stimuli of red-black and green-black chessboard patterns were detected by blood oxygenation level dependent-functional magnetic resonance imaging (BOLD-fMRI) based on block-design and event-related design. Results: The major activated brain regions during visual stimulation with block-design modal were in the visual cortex in both ametropic amblyopic and healthy groups; While under the visual stimulation with event-related design modal, the activation were showed in the brain areas that implicated in visual attentional and conscious modulation such as frontal, cingulated, parahippocampal, precentral and temporal regions besides visual fields in both groups. And the intensity of activated areas in ametropic amblyopic group was lower significantly than that in healthy group. Conclusions: The reduced activities of the neurons or reduced synchronization among activity neurons in visual cortex may be major causes of visual cortical deficit in people with ametropic amblyopia. The decreased activation in the regions which related to visual attention and consciousness in ametropic amblyopic group may suggest that the neural network activities among these brain areas and the roles of these areas on visual awareness and cognition in ametropic amblyopic patients become weaker compared to healthy people.