Abstract Purpose The retinal stages of color processing have been extensively researched in recent years. In contrast, the cortical stages, especially the spatial distribution of visual processing are less understood. It is known that many cells in the visual cortex respond to color. However, what kind of computations these cells perform on their visual input, and what are their temporal and spatial properties are still under debate. In this study, we aimed to analyze the neuronal sources of visually evoked potentials using selective color opponent channel stimulations. Methods The study was conducted on 10 healthy subjects (6 male, 4 female, 1 eye each, mean age 25.5±5.1 yr). All subjects were free of eye diseases. Normal color vision was checked with Ishihara and Stilling-Velhagen plates. To modulate selective activity in the S-cone and L/M-cone driven channels (the related cells are: short-wavelength absorbing: S-cone, medium-wavelength absorbing: M-cone, long-wavelength-absorbing: L-cone) we presented two silent substitution flash sequences (total of 200 stimuli) in a full circle with a diameter of 22°. Electroencephalography was performed using a 64-channel amplifier system (Theraprax, neuroConn GmbH, Germany) in combination with Ag/AgCl ring electrodes (B10-S-200, EASYCAP GmbH, Germany). The preprocessed data were analyzed with source localization software (CURRY v4.6, Compumedics, USA). For each subject, a realistically shaped volume conductor was constructed by a boundary element model. Results We found two main components (N1, P1) in all subjects, as well as a third late component in most subjects. For these components significant latency differences (mean: N1 = 33 ms, P1 = 22 ms; p < 0.05) between both color opponent channels were found. The results showed no differences in the topography and no differences in dipole localization between both color channels. Talairach coordinates of grand averages indicated activation in area 18. Conclusions Our findings showed that neural processing occurs in the same areas of the visual cortex for stimuli with different spectral properties. The signals of S- and L/M-cone driven channels are transmitted in distinct pathways to the cortex. Thus, the observed latency differences might be caused by different anatomical and functional properties of these pathways.