The rat is of increasing importance for experimental studies on fracture healing. The healing outcome of long bone fractures is strongly influenced by mechanical factors, such as the interfragmentary movement. This movement depends on the stability of the fracture fixation and the musculoskeletal loads. However, little is known about these loads in rats. The musculoskeletal loads during gait were estimated using an inverse-dynamic musculoskeletal model of the right hindlimb of the rat. This model was based on a micro-CT scan of the lower extremities and an anatomical study using 15 rat cadavers. Kinematics were reconstructed from X-ray movies, taken simultaneously from two perpendicular directions during a gait cycle. The ground reaction forces were taken from the literature. The muscle forces were calculated using an optimization procedure. The internal forces and moments varied over the gait cycle and along the femoral axis. The greatest internal force (up to 7 times bodyweight) acted in the longitudinal direction. The greatest internal moment (up to 13.8 bodyweight times millimeter) acted in the sagittal plane of the femur. The validity of the model was corroborated by comparing the estimated strains caused by the calculated loads on the surface of the femoral mid-shaft with those from the literature. Knowledge of the internal loads in the femur of the rat allows adjustment of the biomechanical properties of fixation devices in fracture healing studies to the desired interfragmentary movement.