Background The effect of CAG repeats on brain function below disease threshold has not been studied thoroughly. We sought to evaluate the possibility of assortative mating in a group of subjects recruited from the community and with no family history of Huntington’s.

Methods 85 healthy children ages 6–18 years of age were recruited from the surrounding community. The first 47 consecutive subjects were collected and a second set of subjects, n = 38 were enrolled after. These were treated as mutually exclusive samples. DNA was provided and CAG repeat measured. Spearman correlations were run evaluating the relationship between the two alleles in regard to CAG repeat length.

Results The first sample showed a significant correlation of r = 0.511, p = 0.0002, thus longer Allele1 lengths were associated with longer Allele2 lengths. The correlation for the 2nd sample, was similar at r = 0.528, p = 0.0007.

Conclusion This simple analysis shows evidence that there is assortative mating in regard to CAG length of HTT. That is, the length of CAG repeat in the maternal allele of HTT strongly correlates with the length of the CAG repeat of the paternal allele of HTT, suggesting that the male and female pair mated based on the common feature of having a similar genotype (length of CAG repeat).