Human trichromatic vision is based on three classes of cones: L, M, and S (long-, middle-, and short-wavelength sensitive, respectively). Individuals can have more than one M and/or more than one L pigment gene on the X chromosome along with an S pigment gene on chromosome 7. In some people the X-linked pigment gene array can include polymorphic variants that encode multiple, spectrally distinct cone photopigment subtypes. A single-cell, polymerase chain reaction approach was used to examine visual pigment gene expression in individual human cone cells and identify them as L or M. The ratio of L:M pigment gene expression was assayed in homogenized retinal tissues taken from the same eyes. Results indicate that there is a close correspondence between the cone ratio determined from counting single cells and the L:M pigment mRNA ratio estimated from homogenized pieces of retina. The results also show that the different pigment genes in one array are often expressed at very different levels, giving rise to unequal numbers of L and M cones. Expression of only one photopigment gene was detected in each cone cell. However, individual males can have more than the classically described three spectrally distinct cone types in their retinas.