We investigated neuronal correlates of amblyopic deficits resulting from early onset strabismus or anisometropia by monitoring individual responses in retinotopically mapped cortical visual areas with functional magnetic resonance imaging (fMRI) in eight psychophysically assessed adult amblyopes. In lower visual areas (V1/V2), grating stimuli presented to the normal and the amblyopic eye evoked strong cortical responses, while responses to the amblyopic eye were progressively reduced in higher areas on the central visual pathway (V3a/VP; V4/V8; lateral occipital complex, LOC). Selective reduction for high spatial frequency gratings was especially obvious in LOC. This suggests that transmission of activity from the amblyopic eye is increasingly impaired while it is relayed towards higher processing levels. Elevated responses in parts of areas VI and V2 to monocular stimulation of the amblyopic eye might be related to the spatial and temporal distortions experienced by some amblyopic subjects.