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Background: In this prospective case series we have assessed the clinical effects of 8 weeks military training on the lower extremity of the recruits., Materials and Methods: Military recruits who met the eligibility criteria and gave informed consent were entered into the study. They were asked to fill out a self-reporting pain and functionality questionnaire before and after their training. They were also examined by a physician before and after their military training. The questionnaire and examination were concentrated on three blocs: lower back, knee, and foot., Results: Three-hundred and seventy-three study subjects were evaluated. The study showed that there is a significant difference in reporting lower back pain after the training compared to the rate of complaints prior to the training (P < 0.001), knee pain, and foot pain also increased significantly (P < 0.1 and P < 0.0001, respectively) The difference was most prominent in foot complaints. Physical examination also showed significant increase in lower extremity findings following the training (P < 0.05)., Conclusion: Our study shows that there is a need for a new approach to military training of male recruits in Iran in order to minimize the adverse health effects.