Childhood obesity is associated with premature cardiovascular complications. However, little is known about the effect of a family-based behavioural intervention on the relationship between arterial function, blood pressure and biomarkers in pre-pubertal children with obesity. This was a single centre randomized controlled trial (RCT) including 74 children randomized to a 6-month behavioural intervention to treat obesity. In 48 children (13 controls and 35 interventions), we assessed: serum level of cytokine (CCL2), adiponectin, and neutrophil product (MMP-8), as well as carotid intima-media thickness, flow-mediated dilation (FMD), nitroglycerin-mediated dilation; arterial stiffness (incremental elastic modulus, Einc), pulse wave velocity (PWV), resting and 24-hour blood pressure (BP). At baseline, resting systolic BP was positively associated with MMP-8 levels which was significantly higher in children with hypertension (P=0.033). Biochemical markers were not related to endothelial function at baseline, but they globally increased after 6months in the intervention group. The significant increase of CCL2 levels in the intervention group was associated with a decrease in diastolic BP. Furthermore, adiponectin change was positively related to a change in FMD and negatively to change in Einc and PWV. The usefulness of serum biomarkers for the detection of cardiovascular diseases is not well established in children. In our population, MMP-8 concentration was higher in hypertensive children. Furthermore, behavioural interventions resulted in a paradoxical increase in some biomarkers in children, with potentially beneficial effects detected with CCL2 changes. Caution should be taken when using nonspecific serum biomarkers for the clinical monitoring of children with obesity.