PURPOSE: To investigate differences in metatarsal bone structure and training habits in runners with and without a recent metatarsal bone stress injury (BSI). METHODS: Fifty-four runners (14 male/40 female, age 25.8±7.3 yrs) who ran 47±32 kilometers weekly participated in this study. Training and injury history data were collected, along with CT images from metatarsals 2-4 of the non-injured foot of recently injured runners (n=11, 5 male), and the left foot from the healthy runners (n=43, 9 male). Quantitative CT analysis was performed and subject-specific finite element (FE) models simulated a "virtual mechanical test" on each bone at a range of biomechanically relevant angles. Key FE outcomes included principal strains and a measure of total damaged volume, which is related to fatigue life. RESULTS: Injured runners reported significantly higher training volume (78.9±33.9 km/week) than healthy runners (39.2±20.2 km/week) and had lower BMI (21.3±1.7 vs. 22.7±2.6 kg/m2) but the groups were otherwise similar. In the female group, injured runners had significantly larger bone volume and BMC, similar bone strains, and significantly higher damaged volume metrics than healthy females. The FE simulations showed that decreasing the loading angle of the metatarsals by 10 degrees was associated with a 22% decrease in strain and damaged volume. CONCLUSION: The metatarsals of injured and healthy runners are only slightly different from each other, and there are no obvious structural deficits in the injured runners. Other factors including training volume, footstrike biomechanics, and sex differences may explain BSI in this cohort. Interventions that decrease metatarsal loading angle or magnitude may reduce BSI risk by reducing bone microdamage.