Morphologies of bird species often vary along elevation gradients, yet causes of the variation have not been examined experimentally. We investigated variation in morphological traits of the dark-eyed junco Junco hyemalis, breeding at 1,000 m a.s.l. (low-elevation; i.e. low) and 2,000 m asl (high-elevation; i.e. high) in the Rocky Mountains, Canada. Eight morphological traits were measured in free-living birds. We found two consistent differences in populations between elevations: at high-elevation sites, females had longer wings and males had longer tails than birds from low- elevation sites. Other age- and gender- specific results were observed in free-living birds between elevations: tarsi were shorter in high-elevation second year (SY) females and after second year (ASY) males, beak lengths were slightly longer in low-elevation SY females, and high-elevation ASY females tended to have lower fat than low-elevation ASY females. Morphological differences may result from genetic differences between elevations, or phenotypic flexibility resulting from exposure to the different environmental conditions. To identify which mechanism caused the difference in morphometrics, hand-reared birds from low- and high-elevation habitats were raised in identical conditions with unlimited access to high quality food until they had replaced all feathers. The traits measured in the lab (wing and rectrix length, weight and fat score) tended to increase in magnitude compared to field values. Juncos from high- and low-elevations had similar responses to the aviary environment, with one exception: males from high-elevation sites had greater weight gain relative to free-living juncos than males from low-elevation sites. Thus, morphological traits in dark-eyed juncos were phenotypically flexible, capable of growing larger in the laboratory environment. However, there were also persistent genetic or perinatal/maternal differences underlying population responses that prevented traits from converging under aviary conditions. As a result, trait size differences between high- and low-elevation populations were maintained or exacerbated in the common aviary environment.