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Background Racism is a major public health issue and may be associated with several mental health outcomes. However, more epidemiological analyses are necessary on the theme, particularly longitudinal studies. Therefore, we aimed to examine the association between perceived racial discrimination and anxiety symptoms during adolescence and young adulthood in a Brazilian metropolitan area. Methods A five-wave prospective longitudinal study started in 2000. Individuals were aged from 10 to 21 years at baseline, with clustered random sampling. Questions about the experience of racial discrimination were asked. PHQ-9 evaluated anxiety symptoms. Repeated measures analysis with GEE (Generalized Estimating Equations) estimated adjusted relative risks. Results There were 979 adolescents at baseline, with 19.9% (n = 195) reporting perceived racial discrimination and 26.5% (n = 259) with anxiety symptoms. A positive association was found between the perception of racism and anxiety symptoms, after adjustment for sex and age. When adding socioeconomic status, work and adverse environmental conditions, in the final adjusted model, the association was not substantially affected (RR = 1.52; 95% CI: 1.30-1.79). Conclusions The fight against racism and different types of discrimination and racial violence are urgent for public health. To assure high levels of ethical values and respect for fundamental human rights is still a challenge in the Brazilian society, still marked by the historical and shameful experience of slavery. Public policies, including health policies, in particular, must target the elimination racial discrimination as a central topic, reducing its consequences for mental health of black population. Key messages This study advances by adding a longitudinal analysis to a theme with a lack of epidemiological studies, especially longitudinal ones, contributing to the understanding of the association between racism in adolescence and mental health. The findings highlight the urgent need to fight racial discrimination as an ethical paradigm, reducing severe consequences of this type of violence on mental health. [ABSTRACT FROM AUTHOR]