Shock waves (SW) are considered a promising method to treat bone non unions. One potential mechanisms of action is the initiation of local micro‐fractures, which may in turn trigger the start of bone healing. In this study, a set of eight intact rat femurs have been subjected to SWs (peak positive pressure of 40 MPa and peak negative pressure of −8 MPa, PRF of 2 Hz). The number of SW was varied from 50 to 1500. Micro‐CT images of the specimens were acquired before and after treatment (16 microns resolution). In parallel, numerical simulations were used to quantify the stresses induced by SWs in cortical bone tissue. We used a 3‐D FDTD code to solve the linear lossless equations that describe wave propagation in solids and fluids. A 3‐D model of a fractured rat femur was obtained from micro‐CT data. Results demonstrate that damages were induced in the bone tissues from 150 SWs. Comparison of the location of the induced damages on micro‐CT images with predictions of maximum stresses by numerical simulations...