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During pre-adolescence, several variables connected to growth and weight status could influence physical performance and technical skills. This study aims to assess the influence of growth-related anthropometric changes, weight status, and basketball experience on physical performance in pre-adolescent basketball players. The sample consisted of 50 male basketball players (12.2 ± 0.4 years-old) included in the U-13 category. Anthropometric characteristics were collected using standard procedures. Physical performance was evaluated by 20 m Dash, T-test, squat jump, countermovement jump, and medicine ball throw. In order to assess growth-related changes, we conducted two surveys within a 10-week time span. Student's t-test was used to compare the data collected in the two surveys and multiple regression analyses were performed to assess the effects of growth, weight status, and basketball experience on performance. After 10 weeks there was a significant increase in FFM (Fat-Free Mass) and a significant decrease in fat parameters. Moreover, between the two surveys, all motor tests significantly improved. The results of linear regression models showed that changes in %F (percentage of body fat) were significantly associated with speed and agility, while handgrip strength and weight status were associated with upper limb explosive strength. Basketball experience was a significant predictor of all three motor tests. In conclusion, body composition changes, years of experience, and weight status influenced physical performance and players' motor skills ability, especially speed, agility, and upper limb explosive strength.