For selected species, conservation breeding has become integrated into recovery plans, most often through the production of offspring for reintroduction into nature. As these programs increase in size and scope, it is imperative that conservation managers retain the biological integrity of the species. This study investigated the causes of morphological changes that are known to occur in black-footed ferrets (Mustela nigripes) maintained ex situ. In a previous study, ferrets maintained in captivity were 5–10% smaller in body size than pre-captive, in situ animals. In the present study, the authors compared nine morphological characters among ex situ animals and their in situ descendants. Within the ex situ population, cage types were compared to determine whether housing influenced morphometry. Black-footed ferrets born to reintroduced individuals quickly returned to their pre-captive size suggesting that a diminutive morphology ex situ did not have a genetic basis. Furthermore, cage type affected overall body size and shape; ulnas and tibias were as much as 9% shorter for ex situ animals. The authors hypothesise that small cage size and environmental homogeneity inhibit the mechanical stimuli necessary for long bone development. These findings have ramifications for ex situ managers who need to create artificial captive settings that promote natural physical development. In the absence of such an environment, ‘unnatural’ morphologies can result that may contribute to poor fitness or perhaps even domestication.