Morphological abnormalities can be associated with inbreeding depression or heritability in natural populations. We explored a genetic basis for antler and pedicle deformities documented in a population of reintroduced elk (Cervus elaphus) on the Hualapai Indian Reservation in northwestern Arizona. We used 12 microsatellite loci to compare individual multi-locus heterozygosity (IH) and internal relatedness (IR) between bull elk with antler malformations (n = 23) and individuals with normal antler conformation (n = 17). Additionally, we used 3 pairwise relatedness coefficients to determine whether males with deformed antlers were more closely related than males with normal antlers. Mean IH and mean IR were not significantly higher for the group with deformed antlers. Similarly, the relationship between antler malformations and pairwise relatedness also was not significant, suggesting that deformed males did not share the antler trait because of a closer genetic relationship. Other factors, such as nutritional or environmental characteristics, might be associated with the deformities. Further research is necessary to determine the underlying causes of the antler and pedicle malformations documented in the introduced elk herd in northern Arizona.