Heterochromia is a rare phenomenon where one eye is one color and the other eye is a different color, or one eye may be two or more colors. A genetic cause has not been found and it is not related to the pie balding or spotting genes. In most cases the two colors are a result of mix breeding (breeding two different breeds together). This condition is common in certain breeds like Australian Cattle Dogs, Australian Shepherds, Border Collies, Chihuahuas, Dachshunds, Dalmatians, Great Danes (harlequin coat pattern), Shetland Sheepdogs, Siberian Huskies. Merle, piebald, dappled and harlequin coated dogs are more likely to have Heterochromia eyes. 

There are two types of heterochromia:

1. hereditary, meaning the dog is born with it
2. acquired, meaning the eye(s) changed over time most likely due to an inflammatory condition or an injury

There are three variations of hereditary heterochromia in dogs: 

1. Complete, also known as heterochromia irides (one eye is a completely different color than the other eye)
2. Sectoral (part of the dog’s iris is one color and the rest of that eye is a different color)
3. Central (different colors within the iris give a spiked or haloed appearance)

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Heterochromia is a benign condition though dogs with lighter eye colors may squint more in direct sunlight. The condition doesn't affect vision or health, with the exception of Dalmatians where blue eyes are associated with a higher risk of deafness. Heterochromia is possible in any dog, purebred or mixed. It should not be a trait focused on in a breeding program; this will increase inbreeding and doesn't maintain the breed standard.

A perfect example of Complete Heterochromia

A great example of Sectoral Heterochromia