A persons eye color is determined by the type of genes he or she has in his or her DNA. Genes can occur in more than one form. These different forms are called alleles, and each person has two alleles of each gene: one inherited from the mother, and one from the father. In the case of eye color, several different genes may play a part. Each of these genes instructs pigments to be deposited in the iris of the eye, with the various forms (alleles) of the genes differing in how much pigment they demand is deposited. The final eye color a person has is therefore a reflection of how much pigment is present in his or her eyes as determined by the exact combination of alleles the person possesses.

Blue eyes result when very little pigment is deposited in the iris. Therefore, a person will only have blue eyes if the alleles he or she has are the types that do not result in high levels of pigmentation. For example, lets say that a person has two alleles of one of the eye color genes, and that both alleles result in very little pigment being deposited. In this case, ignoring for the moment the other genes that are involved, the person would have blue eyes. Now, compare this to a situation in which the person has one allele of the gene (lets say, from the mother) that codes for little pigment, while the other allele (from the father) codes for a lot of pigment. In this case, the second allele causes a lot of pigment to be put into the eye, resulting in brown eyes-- even though one of the alleles is of the blue-eye type! The second allele puts the pigment in anyway, and covers up the blue eyes of the first allele. In genetic terms, we would say the first allele is recessive, while the second allele is dominant: whenever a dominant allele is present, it covers up the recessive allele in terms of the physical result.

If you think about this, it seems clear why blue eyes are less common around the world. In order to have blue eyes, a person must have only all-blue alleles! If even one brown allele gets in, the person will not have blue eyes. However, this is a little misleading. Although blue is the recessive condition for eyes, it is not true that recessive traits are always less common. Whether the recessive trait or the dominant trait is more common actually depends on which trait provides the person with the best chance to survive and reproduce. In general, brown eyes are more common in people overall, but there are some regions of the world (such as Scandinavia) where blue eyes are actually more common.

The genetic variant ("allele") that causes blue eyes is a mutation in the genome which creates a defective protein that is unable to make the usual brown pigment that makes brown eyes. The mutation appears to have happened or at least been present in the ancestors of the Indo-European people who originated somewhere near the Caucasus Mountains between the Black and CaspianSeas, and spread from there as the Indo-Europeans invaded the lands around them: Europe (the Celts, Scythians, Hellenes, Iberians, etc.), the Middle East (the Hittites, Phonecians, and Persians), India (theAryans), and China (some of the Mongols). Conditions in the far north somehow favored this mutant allele, probably because of the low levels of sunlight at high latitudes. Most of the rest of the world, however, still retains the ancestral condition with brown eyes, either because the allele is not favored at lower latitudes where there is more sun or simply because the Indo-European peoples encountered obstacles that halted their invasions.