The Mexican gray wolf appears to be extinct in the wild and exists now only in captivity and as a reintroduced population in southeast Arizona and southwest New Mexico. A recent study did not find evidence for inbreeding depression in juvenile viability or litter size in captive animals. Here we found that captive wolves with little or no known inbreeding had lower body size than wild-caught wolves. In addition, captive wolves with higher inbreeding had lower body size than captive wolves with little or no inbreeding. The captive population was descended from three founders until two other lineages, each descended from two founders, were recently added to the population. There has been concern that the offspring from matings between these lineages may differ from the individuals in the original lineage so we examined the potential statistical power to detect differences between body size for animals from cross-lineage matings and other matings. In endangered species there are often limited opportunities to obtain sample sizes large enough to detect statistically significant differences because of the extensive resources needed to produce and maintain captive animals. In this case, however, it appears from our examination that in the next few years there will be an adequate sample size to evaluate statistically the differences in body size between these groups.