Persons with spinocerebellar ataxia experience a degeneration of the spinal cord and the cerebellum, the small fissured mass at the base of the brain, behind the brain stem. The cerebellum is concerned with coordination of movements, so the "wasting away" of this critical control center results in a loss of muscle coordination. Atrophy in the spine can bring spasticity.

There are many types of spinocerebellar ataxia and about 30 different gene mutations have been found. One of the common genetic defects is a an expansion of a CAG triplet repeat. In this way, it is similar to fragile-X syndrome, Huntington disease and myotonic dystrophy, all of which exhibit a triplet repeat expansion of a gene. In the case of spinocerebellar ataxia I, the gene is SCA1, found on chromosome 6. The protein product of the gene - called ataxin-1 - varies in size, depending on the size of the CAG triplet repeat.

A homolog of human ataxin-1 has been found in mice, where it is found on chromosome 13 instead of chromosome 6. The two proteins are highly similar, except that in the mouse, the poly-glutamine tract (coded for by the CAG repeat ) is missing, suggesting that it is not essential for normal function in mice.