Mechanical loads play a significant role in determining long bone shape and strength, but less work has explored how these loads influence flat bones like the scapula, which has been shown to vary with locomotor preference among primate taxa. Here, we tested the effects of voluntary running and climbing exercise in mice to examine how the mechanical loads borne from different locomotor patterns influence shoulder morphological development. Ninety-nine female wild-type mice were distributed equally among sedentary control, activity-wheel running, and vertical climbing experimental conditions. Running mice had the lowest body masses, larger intrinsic shoulder muscles, and the most pronounced differences in scapular size and shape relative to the other groups. Climbing mouse scapular morphology also differed significantly from the control individuals, but these differences were not as marked as those between the running and control mice. This might be attributable in part to greater levels of activity in the wheel-runners relative to the climbers. Additionally, climbing mice held their bodies closer to the substrate and maintained more flexed limbs and posterior hand positions compared with the kinematics of running. As a result, climbers differed significantly from both the running and control mice in developing a relatively broader infraspinous region, which is likely related to preferential recruitment of the infraspinatus and teres minor muscles to maintain flexed shoulder postures. The results of this study demonstrate that variation in activity level and type of locomotor regime over a significant portion of the life history influences muscle and bone development in the shoulder. J. Exp. Zool. (Mol. Dev. Evol.) 9999B:621–638, 2012. © 2012 Wiley Periodicals, Inc.