We assessed the locomotor performance of captive northern flying squirrels (Glaucomys sabrinus) over short glide distances and on small branches. We used stroboscopic photography, digital video, and an instrumented force pole to estimate takeoff and landing forces, angle of attack, and velocity profiles over short glides. We determined stride phases and duty factors of the animals as they moved across small branches, and compared these results with those for a small marsupial glider. Launch velocity, initial acceleration, and glide angle were not related significantly to animal mass. Initial velocity, terminal velocity, and landing force increased with increasing glide distance. Angle of attack at launch was not related to glide distance, but at landing it increased with increasing distance, suggesting active stalling. Simultaneous observations of takeoff and landing forces suggest that at distances greater than 2 m, landing forces are smaller than takeoff forces. The flying squirrels did not demonstrate a high level of agility as they traversed small branches. As branch diameter decreased below 2.5 cm, duty factors were greater than 0.5, indicating use of a walking gait. In comparison, small marsupial gliders (Petaurus breviceps) used running gaits with duty factors less than 0.5 for the same branches. We used relative warp analysis to explore pelvic and femoral shape variation in flying squirrels, and relate these to differences in locomotor performance. Small squirrels such as Glaucomys appear to have a pelvic and femoral architecture that has greater mechanical advantage for leaping than large squirrels such as Petaurista. We interpret these differences in the context of predator avoidance and foraging strategies.