SummaryBackground. The origin of atypical femoral fractures (AFF) associated with bisphosphonate therapy remains to be elucidated. In this study, a biopsy of an AFF site is analyzed to determine whether microdamage and/or morphological changes are present in the area of the AFF. Material and methods. Cortical bone from an AFF region was obtained during a preventive stabilization in a patient with a symptomatic AFF. This bone was scanned using microCT (resolution=0.01 mm), stained with basic fuchsin and analyzed histologically. Results. The diameter of the Haversian canals was higher in the vicinity of the AFF compared to the bone further away from the AFF. The bone mineral density within the cortex ranged from 1020 to 1080 mg HA/cm 3 . We observed penetration of basic fuchsin into the matrix, which is a tell-tale sign of diffuse damage. Discussion. The higher diameter of haversian canals is likely to result in higher local stresses and consequently increased microdamage. The diffuse microdamage in the biopsy may furthermore be directly related to bisphosphonate use, preventing repair of microdamage, and consequently the development of the AFF. Conclusion. Increased porosity of the cortex and accumulation of microdamage might have lead to a stress fracture and ultimately a complete AFF.