Mechanisms of color vision in cortex have not been as well characterized as those in sub-cortical areas, particularly in humans. We used fMRI in conjunction with univariate and multivariate (pattern) analysis to test for the initial transformation of sub-cortical inputs by human visual cortex. Subjects viewed each of two patterns modulating in color between orange-cyan or lime-magenta. We tested for higher order cortical representations of color capable of discriminating these stimuli, which were designed so that they could not be distinguished by the postulated L-M and S-(L + M) sub-cortical opponent channels. We found differences both in the average response and in the pattern of activity evoked by these two types of stimuli, across a range of early visual areas. This result implies that sub-cortical chromatic channels are recombined early in cortical processing to form novel representations of color. Our results also suggest a cortical bias for lime-magenta over orange-cyan stimuli, when they are matched for cone contrast and the response they would elicit in the L-M and S-(L + M) opponent channels.