Multiple threshold algorithms applied to microcomputed tomography analysis were used to probe the effects of low‐intensity pulsed ultrasound on fracture healing. Rat femurs were fractured in accordance with IACUC guidelines. Ultrasound treatment was administered daily to one femur; the contralateral bone was treated with a sham transducer. Each week for 3 weeks healing fractures were harvested and scanned by micro‐CT. Remodeling activity was confirmed by evaluation of TRAP activity. Using thresholds of 331–700 and 225–330, area of cortical bone, and new bone formation, respectively, were identified, and by inference, regions of bone resorption. The increased sensitivity of this multithresholding procedure revealed that ultrasound treatment significantly increased the rate of fracture healing in vivo by activating both new bone formation and by increasing the removal of cortical bone in a time‐ and site‐specific manner. At week 1, compared to the proximal side, there was a significant increase in new bone formation distal to the fracture site. Removal of the existing cortical bone followed the same pattern at week 2. Results of the study indicate that at sites of bone turnover, this multithresholding analytical technique can be used to provide quantitative information on bone formation, as well as resorption. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27: 673–679, 2009