Why are puppies born with blue eyes? The reason why puppies have blue eyes when they are born is quite simple, it comes down to a lack of melanin in their irises, which only begins to develop as they get older. Due to this absence of melanin, their eyes appear to look bluish, however, they are more of a clear color. To further expand on this, the blue appearance in their irises is caused by the lack of melanin coupled with the refraction and reflection of light.