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Stress fracture is a common overuse injury within military training, resulting in significant economic losses to the military worldwide. Studies to date have failed to fully identify the bone density and bone structural differences between stress fractured personnel and controls due to inadequate adjustment for key confounding factors; namely age, body size and physical fitness; and poor sample size. The aim of this study was to investigate bone differences between male Royal Marine recruits who suffered a stress fracture during the 32 weeks of training and uninjured control recruits, matched for age, body weight, height and aerobic fitness. A total of 1090 recruits were followed through training and 78 recruits suffered at least one stress fracture. Bone mineral density (BMD) was measured at the lumbar spine (LS), femoral neck (FN) and whole body (WB) using Dual X-ray Absorptiometry in 62 matched pairs; tibial bone parameters were measured using peripheral Quantitative Computer Tomography in 51 matched pairs. Serum C-terminal peptide concentration was measured as a marker of bone resorption at baseline, week-15 and week-32. ANCOVA was used to determine differences between stress fractured recruits and controls. BMD at the LS, WB and FN sites was consistently lower in the stress fracture group (P<0.001). Structural differences between the stress fracture recruits and controls were evident in all slices of the tibia, with the most prominent differences seen at the 38% tibial slice. There was a negative correlation between the bone cross-sectional area and BMD at the 38% tibial slice. There was no difference in serum CTx concentration between stress fracture recruits and matched controls at any stage of training. These results show evidence of fundamental differences in bone mass and structure in stress fracture recruits, and provide useful data on bone risk factor profiles for stress fracture within a healthy military population., (Crown Copyright © 2014. Published by Elsevier Inc. All rights reserved.)