The aetiology of stress fractures is multifactorial, and many risk factors have been implicated. The aim of this study was to explore the relationship between stress fractures, factors and biochemical markers related to bone metabolism, and calcaneal stiffness index measured by quantitative ultrasound in a case control study including male military personnel beyond basic training. Thirty-two male patients with stress fractures were matched with 32 uninjured-healthy volunteers by age, height, body weight and level of physical performance. A questionnaire concerning the calcium intake, alcohol consumption and smoking was completed, the values of several biochemical markers were measured from blood samples, and calcaneal quantitative ultrasound was measured by heel ultrasound for all participants. Statistically significant higher levels of albumin (4.59 +/- 0.28 vs. 4.40 +/- 0.25, p = 0.006) and lower levels of serum osteocalcin (6.26 +/- 1.74 vs. 7.40 +/- 1.80, p = 0.012), mean values of T-scores (- 0.21 +/- 0.95 vs. 0.33 +/- 0.82, p = 0.018) and Z-scores (- 0.14 +/- 0.81 vs. 0.33 +/- 0.71, p = 0.016) were found among patients compared to controls. Based on the results, it seems that a decreased bone turnover and a low calcaneal stiffness index may be related to the incidence of stress fractures amongst male military personnel.