Regular and planned physical activity can diminish the risk of numerous illnesses. However, school children and teenagers often exercise intermittently and for brief periods, restricting potential benefits. Furthermore, previous studies mainly focused on body composition, without providing molecular mechanisms elucidating the role of physical activity in muscle tissue and inflammatory signalling. The objective of this study was to determine the effect of a vigorous physical activity intervention on endocrine muscle function and cytokine output in children. 103 boys were divided into two groups: control (n=51, did not perform additional physical activity) and exercise (n=52, performed vigorous physical activity). Body composition measurements, endocrine muscle function and inflammatory signalling biomarkers were assessed at enrolment and after 6 months of intervention. No statistical significance was found for fractalkine, oncostatin, EGF, TNF-α and eotaxin. However, LIF, FBAP3, IL-6, FGF21 and IL-15 increased in the exercise group at the end of the protocol, though myostatin got decreased. In contrast, IFN-γ was increased in the exercise group at the beginning and end of the exercise protocol, IL-10 was also increased in this group, IL-1α decreased in the exercise group before and after the exercise protocol, and IP-10 and MCP-1 also decreased in the exercise group. It can be affirmed that a physical activity programme for boys was shown to produce changes in body composition (decreased fat mass, increased lean mass) and in markers of endocrine muscle function and cytokine release. It is possible that these changes, if sustained, could reduce the risk of chronic disease.