In seven families from a Siberian founder population with autosomal dominant spinocerebellar ataxia (SCA) genetic analysis of the polymorphisms flanking the SCA1 locus on chromosome 6p showed allelic association with disease inheritance. While the association was absolute in the case of microsatellite D6S274, an allele switch was observed for D6S89 in two families, suggesting a historic recombinant. Further genetic and physical study of this recombinant event could be instrumental for the precise localization and identification of the SCA1 gene.