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Lower limb stress fractures (SF) have a high prevalence in female athletes of running-related sports. The purpose of this study was to investigate bone quality, including bone microarchitecture and strength, and muscle strength in athletes diagnosed with SF.Female athletes with lower limb SF (SF subjects, n = 19, 18-45 yr, premenopausal) and healthy female athletes (NSF subjects, n = 19) matched according to age, sport, and weekly training volume were recruited. Bone microarchitecture of all participants was assessed using high-resolution peripheral quantitative computed tomography at two skeletal sites along the distal tibia of the dominant leg. Bone strength and load distribution between cortical and trabecular bone was estimated by finite element analysis. Using dual-energy x-ray absorptiometry, areal bone mineral density (aBMD) at the hip, femoral neck, and spine was measured. Muscle torque (knee extension, plantarflexion, eversion/inversion) was assessed (Biodex dynamometer) as a measure of lower leg muscle strength.SF subjects, after adjusting for body weight, had thinner tibia compared with NSF subjects as indicated by a lower tibial cross-sectional area (−7.8%, P = 0.02) and higher load carried by the cortex as indicated by finite element analysis (4.1%, P = 0.02). Further site-specific regional analysis revealed that, in the posterior region of the tibia, SF subjects had lower trabecular BMD (−19.8%, P = 0.02) and less cortical area (−5.2%, P = 0.02). The SF group exhibited reduced knee extension strength (−18.3%, P = 0.03) compared with NSF subjects.These data suggest an association of impaired bone quality, particularly in the posterior region of the distal tibia, and decreased muscle strength with lower limb SF in female athletes.