http://www.strabismus.org/what_causes_strabismus.html
This document lists the many things and/or events that can cause a strabismus. They include genetics, inappropriate development of the "fusion center" of the brain, problems with the controlled center of the brain, injuries to muscles or nerves or other problems involving the muscles or nerves. The document also discusses what happens if a person's two eyes are not aligned (strabismic), including double vision, suppression, and anomalous retinal correspondence.