Introduction Determinants of BUA and SOS and their changes during military service-associated physical training were studied in 196 army recruits and 50 control men, aged 18-20 years. Methods Heel ultrasound measurement, DXA, muscle strength test, Cooper's running test and genetic analyses were performed. Lifestyle factors were recorded. Sex steroids and bone turnover markers were determined. Heel ultrasound was repeated after six months. Results Exercise was the most significant determinant of both BUA (p < 0.0001) and SOS (p < 0.0001). There were 10% and 1.3% differences in BUA (p=0.006) and SOS (p=0.0001), respectively, between men belonging to the lowest and highest quartiles of exercise index. Weight associated with BUA (p=0.005) and height with SOS (p=0.03). BUA and SOS correlated with BMC and BMD (p < 0.0001) but explained only up to 21% of their variance. Over six months SOS increased more in recruits than in control men (p=0.0043), the increase being higher, the lower muscle strength at baseline (r=-0.27, p=0.0028). Conclusion Exercise is the most important determinant of ultrasonographic variables in men, aged 18-20 years. Physical loading during military training increases SOS.