Fluctuating asymmetry has been proposed as a measure of developmental homeostasis and an indicator of populations under stress. However, controversy surrounds not only the validity of an association between fluctuating asymmetry and levels of protein heterozygosity, but also whether fluctuating asymmetry can be used to identify populations under genetic and environmental stress, The relationship between levels of heterozygosity and developmental homeostasis is considered by comparing levels of cranial fluctuating asymmetry in three tamarin samples with contrasting levels of heterozygosity: (1) low heterozygosity cotton-top tamarins (N = 324), (2) presumably normally heterozygous Illiger's saddle-back tamarins (N = 208), and (3) relatively highly heterozygous hybrids between saddle-back tamarin subspecies (N = 31). All specimens originated at the Oak Ridge Associated Universities' Marmoset Research Center. A nested ANOVA design was used to separate out variation due to individual differences, side-to-side differences (fluctuating asymmetry), and measurement error. We found statistically significant levels of fluctuating asymmetry in nearly all of the traits surveyed and a negative correlation between levels of fluctuating asymmetry and genetic heterozygosity. Efforts to use fluctuating asymmetry to identify populations endangered by reduced genetic variability and/or under stress may be inhibited by small sample sizes, neglect of repeated measures, and lack of appropriate reference populations.