A subgroup of trinucleotide repeat diseases result from abnormal expansions of CAG repeats which are translated into polyglutamine stretches. As yet there is little understanding of how the polyglutamines function either normally, or when expanded. We have investigated these sequences in the Machado-Joseph disease, androgen receptor and spinocerebellar ataxia type 1 genes in humans and other primates. None of the 748 normal chromosomes that were examined had more than 34 uninterrupted glutamine codons in the Machado-Joseph disease gene. Similarly, no normal alleles with more than 39 uninterrupted glutamine codons have been reported for the other disease genes associated with polyglutamine expansions. Sequence analyses of the repeats in primates revealed shorter polyglutamine stretches in some of the non-human primates at all three loci and marked diversions from the expected polyglutamines in the orang-utan Machado-Joseph gene and in the marmoset spinocerebellar ataxia type 1 gene. These data suggest that conservation of these polyglutamine stretches may not always be necessary for normal gene function.