Background <p>The global rise in overweight and obesity among children and adolescents represents a major public health challenge. Although regular physical activity may mitigate excessive weight gain, excess body weight is also observed among youth participating in organized sport. This study aimed to describe the trends and patterns in body mass index categories among young athletes in Estonia from 2010 to 2024.</p> Methods <p>The sample comprised 40,077 pre-participation examination records of young athletes from various sports disciplines, including 25,696 examinations in boys and 14,381 in girls. Subjects were 8–19 years old, who underwent sports medical health evaluations at Tartu University Hospital. Body mass index was classified according to WHO body mass index-for-age reference standards. Statistical analyses included descriptive statistics, chi-square tests, correlation analyses, and logistic regression.</p> Results <p>Differences in body mass index categories were observed across all age groups and sport disciplines, with consistently higher prevalence of excess body weight among boys than girls. Among boys, the combined prevalence of overweight and obesity ranged from approximately 19% to 22% across calendar years, whereas among girls the corresponding range was approximately 12% to 15%. Age-adjusted logistic regression revealed no significant temporal trend in either sex between 2010 and 2024. Distinct age-related patterns were evident: in boys, obesity prevalence was highest at younger ages and declined with age, while in girls the prevalence of overweight and obesity increased from childhood to mid-adolescence. Prevalence varied markedly by sport discipline, being higher in ball games and speed-strength sports and lowest in aesthetic sports. Weekly training hours were negatively associated with body mass index category in boys (ρ = -0.072, <i>p</i> &lt; 0.001) and girls (ρ = -0.132, <i>p</i> &lt; 0.001), and exercise tolerance was inversely associated with body mass index category in both sexes.</p> Conclusions <p>Excess body weight affects a meaningful proportion of young athletes in Estonia despite regular participation in organized sport. Although prevalence was lower than in the general youth population, marked differences by sex, age, and sport discipline identify specific risk groups. These findings suggest the need for targeted prevention strategies integrated into youth sport settings, including appropriate monitoring of growth and development, fitness, and body composition and early intervention for athletes at increased risk.</p> Trial registration <p>Clinical trial number: not applicable.</p>