Molecular evidence strongly supports the derivation of flying squirrels from tree squirrels, with the sister group being the Holarctic tree squirrels (Sciurus) and their close relatives. We present a rationale for the hypothesis that the transition occurred among small squirrels, and we propose using the northern flying squirrel (Glaucomys sabrinus) and the southern flying squirrel (Glaucomys volans) as models. Thus, we compare their morphologies with similar-sized tree squirrels (the Central American dwarf squirrel [Microsciurus alfari] and the western dwarf squirrel [M. mimulus]). We compare body proportions of Glaucomys with those of Microsciurus, considering differences as potential adaptations for gliding associated with wing loading, aspect ratio, and parasitic drag. We use the following measurements: lengths of the centra of the thoracic, lumbar, sacral, and caudal vertebrae; and lengths of the long bones (humerus, radius, femur, and tibia), metacarpals, metatarsals, and proximal phalanges of the hands and feet. We then compare these proportions of Microsciurus with those of other species of Sciurini, and the proportions of Glaucomys with other species of Pteromyini, to determine if each is representative or derived within its clade. Members of the genus Glaucomys exhibit relative elongation of the lumbar vertebrae and the forearm, relevant to wing loading and aspect ratio, relative lengthening of the midcaudal vertebrae, and relative shortening of the more distal caudal vertebrae, perhaps of importance for stability and control. Members of the genus Glaucomys also have shorter hands and feet, but these appeared to be elongated in Microsciurus, rather than shortened in Glaucomys, leaving the issue of parasitic drag moot. Finally, we speculate on the genetic changes that have produced these morphological modifications and may facilitate the evolution of gliding flight.