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Background: Despite recommendations on how to prevent baseball injuries in youths by the Japanese Society of Clinical Sports Medicine, shoulder and elbow pain still frequently occurs in young baseball players. We conducted a questionnaire survey among baseball players at elementary schools across the country to understand the practice conditions of players, examining the risk factors of shoulder and elbow pain in baseball players. Methods: The questionnaire survey was conducted among elementary school baseball players as members of the Baseball Federation of Japan in September 2015. Results: A total of 8354 players belonging to 412 teams (average age: 8.9) responded to the survey. Among 7894 players who did not have any shoulder and/or elbow pain in September 2014, elbow pain was experienced in 12.3% of them, shoulder pain in 8.0% and shoulder and/or elbow pain in 17.4% during the previous one year. A total of 2835 (39.9% of the total) practiced four days or more per week and 97.6% practiced 3 h or more per day on Saturdays and Sundays. The risk factors associated shoulder and elbow pain included a male sex, older age, pitchers and catchers, and players throwing more than 50 balls per day. Conclusions: It has been revealed that Japanese elementary school baseball players train too much. Coaches should pay attention to older players, male players, pitchers and catchers in order to prevent shoulder and elbow pain. Furthermore, elementary school baseball players should not be allowed to throw more than 50 balls per day. Study design: Retrospective cohort study.