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In order to understand any observations on iris color change one must understand the process of developing color in the iris of the eye. The base color of the iris is made up of very dark pigmented cells that are at the underside of the iris which reflect back visual blue light, thus giving the appearance of a blue eye. In albinos, the lack of pigment allows light to reflect off the blood vessels giving a pink reflection. It is the level of pigment in the upper (exterior) levels of the iris that give variation on eye colors from blue-green to dark brown. Just as genes are influential on the level of pigmentation of the skin, so genes have influence on eye color, and the structure of the iris.

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Geneticists have designed a model using the bey 2 and gey gene pairs that explains the inheritance of blue, green and brown eyes. In this model the bey 2 gene has a brown and a blue allele. The brown allele is always dominant over the blue allele so even if a person is heterozygous (one brown and one blue allele) for the bey 2 gene on chromosome 15 the brown allele will be expressed. The gey gene also has two alleles, one green and one blue. The green allele is dominant to the blue allele on either chromosome but is recessive to the brown allele on chromosome 15. This means that there is a dominance order among the two gene pairs. If a person has a brown allele on chromosome 15 and all other alleles are blue or green the person will have brown eyes. If there is a green allele on chromosome 19 and the rest of the alleles are blue, eye color will be green. Blue eyes will occur only if all four alleles are for blue eyes. This model explains the inheritance of blue, brown and green eyes but cannot account for gray, hazel or multiple shades of brown, blue, green and gray eyes. It cannot explain how two blue-eyed parents can produce a brown-eyed child or how eye color can change over time. This suggests that there are other genes, yet to be discovered, that determine eye color or that modify the expression of the known eye color genes.

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