Serum inflammatory markers have been studied in adults with anxiety and depression, but little is known about cytokine levels in young adolescents with emotional disorders. The objective of this study is to compare serum levels of interleukin-6 (IL-6) and interleukin-10 (IL-10) between adolescents with internalizing disorders and adolescents from the same community without internalizing disorders. A total of 134 non-medicated subjects (n = 76 with internalizing disorders) were recruited from a larger sample of 2457 individuals. Serum levels of IL-6 and IL-10 were quantified and psychiatric diagnosis was evaluated using structured clinical interviews. Adolescents with internalizing disorders presented significantly higher levels of IL-6 as compared to youngsters without internalizing disorders. Differences between groups in IL-10 levels were not statistically significant. This study points out that IL-6 levels may be associated with internalizing disorders in youths and suggests that inflammation might be an early biomarker of emotional distress. High levels of cytokines may adversely affect general health in the long-term, which raise broader issues in terms of public health if results are replicated.