A range of wavelengths of light stimulates each of these receptor types to varying degrees. Yellowish-green light, for example, stimulates both L and M cones equally strongly, but only stimulates S-cones weakly. Red light, on the other hand, stimulates L cones much more than M cones, and S cones hardly at all; blue-green light stimulates M cones more than L cones, and S cones a bit more strongly, and is also the peak stimulant for rod cells; and violet light stimulates almost exclusively S-cones. The brain combines the information from each type of receptor to give rise to different perceptions of different wavelengths of light.

The pigments present in the L and M cones are encoded on the X chromosome; defective encoding of these leads to the two most common forms of color blindness. The OPN1LW gene, which codes for the pigment that responds to yellowish light, is highly polymorphic (a recent study by Verrelli and Tishkoff, 2004, found 85 variants in a sample of 236 men), so up to ten percent of women  have an extra type of color receptor, and thus a degree of tetrachromatic color vision.Variations in OPN1MW, which codes for the bluish-green pigment, appear to be rare, and the observed variants have no effect on spectral sensitivity.

Color processing begins at a very early level in the visual system (even within the retina) through initial color opponent mechanisms. Opponent mechanisms refer to the opposing color effect of red-green, blue-yellow, and light-dark. Visual information is then sent back via the optic nerve to the optic chiasm: a point where the two optic nerves meet and information from the temporal (contralateral) visual field crosses to the other side of the brain. After the optic chiasm the visual fiber tracts are referred to as the optic tracts, which enter the thalamus to synapse at the lateral geniculate nucleus (LGN). The LGN is segregated into six layers: two magnocellular (large cell) achromatic layers (M cells) and four parvocellular (small cell) chromatic layers (P cells). Within the LGN P-cell layers there are two chromatic opponent types: red vs. green and blue vs. green/red.

After synapsing at the LGN, the visual tract continues on back toward the primary visual cortex (V1) located at the back of the brain within the occipital lobe. Within V1 there is a distinct band (striation). This is also referred to as "striate cortex", with other cortical visual regions referred to collectively as "extrastriate cortex".It is at this stage that color processing becomes much more complicated.

Visual pathways in the human brain. The ventral stream (purple) is important in color recognition. The dorsal stream (green) is also shown. They originate from a common source in visual cortex. In V1 the simple three-color segregation begins to break down. Many cells in V1 respond to some parts of the spectrum better than others, but this "color tuning" is often different depending on the adaptation state of the visual system. A given cell that might respond best to long wavelength light if the light is relatively bright might then become responsive to all wavelengths if the stimulus is relatively dim. Because the color tuning of these cells is not stable, some believe that a different, relatively small, population of neurons in V1 is responsible for color vision.