Susan J. Gross, co-director of the Division of Reproductive Genetics at the Montefiore Medical Center and an associate professor at Albert Einstein College of Medicine, provides this explanation.
Eye color is a manifestation of the pigment that is present in the iris. Brown eyes are rich in melanin deposits, and blue eyes indicate a lack of melanin. The melanocytes of the iris rest in a richly innervated psuedosyncytium, which is necessary to maintain eye color. Two genes control eye color: EYCL3, found on chromosome 15, which codes for brown/blue eye color (BEY), and EYCL1, found on chromosome 19, which codes for green/blue eye color (GEY). Although previously believed to be inherited in simple Mendelian fashion, eye color has proved to be a polygenic trait. Precisely how these genes interact to provide the full constellation of colors, such as hazel and gray, is as yet unknown. Furthermore, other genes may determine the pattern and placement of pigment in the iris, thereby accounting for solid brown as opposed to rays of color.
Heterochromia iridium (two different-colored eyes within a single individual) and heterochromia iridis (a variety of color within a single iris) are relatively rare in humans and result from increased or decreased pigmentation of the iris. Most cases are isolated and sporadic, conceivably resulting from an alteration in the expression of the above-mentioned genes (and those we have yet to find) within the cells of the entire iris or even a particular section. Other potential causes include trauma around the time of birth or later in life, congenital pigmented nevi or even medications such as those used in the treatment of glaucoma. There are a few well-known syndromes of which heterochromia iridis is a striking feature. Waardenburg syndrome type 1, an autosomal dominant disorder caused by mutations in the PAX3 gene, is characterized by pigmentary disturbances of the iris, hair and skin, as well as congenital sensorineural hearing loss. But two different eye colors tends to be an isolated finding, which adds to the seemingly endless and fascinating variation in humans' physical characteristics.