Body size and morphology are key fitness-determining traits that can vary genotypically. They are likely to be important in social insect queens, which mate in swarms and found colonies independently, but genetic influences on queen morphology have been little investigated. Here, we show that the body size and morphology of queens are influenced by their genotype in the leaf-cutting ant Acromyrmex echinatior, a species in which certain lineages (patrilines) bias their development towards reproductive queens rather than sterile workers. We found no relationship between the queen-worker skew of patrilines and the size or morphology of queens, but there was a significant relationship with fluctuating asymmetry, which was greater in more queen-biased patrilines. Our results suggest that queen-biased patrilines do not incur a fitness cost in terms of body size, but may face more subtle costs in developmental stability. Such costs may constrain the evolution of royal cheating in social insects.