Strabismus (misalignment of the eyes; also known as "squint") comprises a common heterogeneous group of disorders characterised by a constant or intermittent ocular deviation often associated with amblyopia (uniocular failure of normal visual development) and reduced or absent binocular vision. The associated poor cosmetic appearance may also interfere with social and psychological development. Extensive twin and family studies suggest a significant genetic component to the aetiology of strabismus. The complexity of the molecular basis of strabismus is now beginning to be elucidated with the identification of genetic loci and disease causing genes. Currently greater insights have been gained into the incomitant subtype (differing magnitude of ocular misalignment according to direction of gaze), whereas less is known about the pathogenesis of the more common childhood concomitant strabismus. It is hoped that a greater understanding of the molecular genetics of these disorders will lead to improved knowledge of disease mechanisms and ultimately to more effective treatment. The aim of this paper is to review current knowledge of the molecular genetics of both incomitant and concomitant strabismus.