Objectives: The objectives of our study were to determine the effect of strenuous physical training on the prevalence of iron deficiency anemia (IDA), iron deficiency (ID) with normal hemoglobin (Hb), and anemia without ID. Methods: Our study was a prospective observational study. We followed 115 healthy male recruits in the Israel Defense Forces elite units during 15 months of training. Blood samples were collected at recruitment and at 6-, 9- and 15-month follow-ups. Results: Upon recruitment, anemia (Hb < 14 g/dL), ID, and ID anemia (IDA) were diagnosed in 28, 31, and 9% of individuals, respectively. Sixty-three subjects (54%) were followed for 6 months; 9 of them (14%) developed new-onset IDA. Among them, the prevalence of anemia rose from 19 to 52%, and ID from 33 to 35%. At the 15-month follow-up, 29% had developed new-onset IDA and 65% showed evidence of ID. Conclusion: We report a high prevalence of anemia, ID, and IDA among young healthy males participating in prolonged strenuous training programs. These findings can be partly explained by the physiological changes associated with strenuous physical activity. Further investigations aiming to develop specific diagnostic guidelines for this unique population are warranted.