Objective: To investigate the relationship between serum alanine transaminase (ALT) and carotid intima media thickness (cIMT) in adolescents, providing evidence for early prevention and control strategies for cardiovascular structural abnormalities in adolescents. Methods: Data were obtained from the third follow up survey (from October to November 2023) of the "Huantai Children Cardiovascular Health Cohort", including 1 153 healthy adolescents with complete information. Analysis of variance (ANOVA) was used to compare cIMT across different ALT level groups, and multiple linear regression was employed to analyze the relationship between serum ALT levels and cIMT. Results: Significant differences in cIMT were observed among Q 1, Q 2, and Q 3 ALT level groups [(0.56±0.04) (0.57±0.04) (0.59±0.04)mm, respectively; F=3.61, P <0.01]. After adjusting for covariates, multiple linear regression revealed a positive correlation between ALT levels and cIMT ( β=0.18, P <0.01). Gender subgroup analysis showed similar results in males ( β=0.19, P <0.01), but no statistically significant association was found in females ( β=0.07, P = 0.54). Conclusions Elevated serum ALT levels are associated with an increased risk of vascular structural damage in adolescents, especially in boys. Early detection and control of abnormal serum ALT levels can help to reduce early vascular structural damage and further reduce the risk of adverse cardiovascular events.