To delineate the fidelity of the functional cortical organization in humans with amblyopia, we undertook an investigation into how spatial information is mapped across the visual cortex in amblyopic observers. We assessed whether the boundaries of the visual areas controlled by the amblyopic and fellow fixing eye are in the same position, the fidelity of the retinotopic map within different cortical areas and the average receptive field size in different visual areas. The functional organization of the visual cortex was reconstructed using a fMRI phase-encoded retinotopic mapping analysis. This method sequentially stimulates each point in the visual field along the axes of a polar-coordinate system, thereby reconstructing the representation of the visual field on the cortex. We found that the cortical areas were very similar in normals and amblyopes, with only small differences in boundary positions of different visual areas between fixing and fellow amblyopic eye activation. Within these corresponding visual areas, we did find anomalies in retinotopy in some but not all amblyopes that were not simply a consequence of the poorer functional responses and affected central and peripheral field regions. Only a small increase in the average (or collective) receptive field size was found for full-field representation in amblyopes and none at all for central field representation. The former may simply be a consequence of the poorer functional responses.