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Background Anxiety and depressive disorders occur in all stages of life and are the most common childhood disorders. However, only recently has attention been paid to mental health problems in indigenous children and studies of anxiety and depressive disorders in these children are still scarce. This study compares the prevalence of anxiety and depressive symptoms in Aymara and non-Aymara children. Among the Aymara children, the study examines the relations between these symptoms and the degree of involvement with Aymara culture. Methods We recruited 748 children aged 9 to 15 years from nine schools serving low socioeconomic classes in the city of Arica, in northern Chile. The children were equally divided between boys and girls and 37% of the children were Aymara. To evaluate anxiety and depressive symptoms we used the Stress in Children (SiC) instrument and the Children Depression Inventory-Short version (CDI-S), and used an instrument we developed to assess level of involvement in the Aymara culture. Results There was no significant difference between Aymara and non-Aymara children on any of the instrument scales. Dividing the Aymara children into high-involvement (n = 89) and low- involvement (n = 186) groups, the low-involvement group had significantly higher scores on the Hopelessness subscale of the CDI-S (p = 0.02) and scores of marginally higher significance in overall Anxiety on the SiC (p = 0.06). Conclusions Although Aymara children have migrated from the high Andean plateau to the city, this migration has not resulted in a greater presence of anxiety and depressive symptoms. Greater involvement with the Aymara culture may be a protective factor against anxiety and depressive symptoms in Aymara children. This point to an additional benefit of maintaining cultural traditions within this population. [ABSTRACT FROM AUTHOR]