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Background: With growing number of females accepted for combat-related military duties in Israel, the special needs of these women should be addressed. Previous studies on women in combat training have found a high prevalence of iron deficiency at recruitment, as well as an increased rate of Stress Fractures (SF) and overuse injuries during training in comparison with men. The aim of this study was to assess the association between hematological and inflammatory variables and stress fracture occurrence among military recruits during basic training. Methods: We followed 3 companies of females and males inducted to a gender integrated light infantry unit, prospectively. Females inducted for a medics and dental assistants’ courses served as controls. Hemoglobin, iron, transferrin, ferritin, CRP and IL-6 levels were measured for all participants, at recruitment, and after 2 and 4 months of training. SF’s were diagnosed radiographically or scintigraphically according to the IDF protocol. Results: 227 female combatants, 83 male combatants and 128 female controls were recruited. At induction, 18% of the female combatants had anemia compared with 8% of the males and 19% of the female controls. Iron deficiency was noted in 40%, 6%, and 38% respectively. There were no clinically significant changes during training. Twelve percent of female combatants developed stress fractures, while there were no occurrences of SF among the male combatants or female controls. Subjects with SF had significantly lower levels of serum iron and iron saturation. Conclusions: A relatively high incidence of anemia as well as iron deficiency was found in this young asymptomatic cohort, with no significant change during training. The lower stores of iron in the female combatants with stress fractures warrants further investigation.