Background The main objective of this study was to describe the inflammatory status of adolescents with Down syndrome (DS) and their relationship with adiposity. Methods Ninety-five adolescents with DS (44.2% girls) and a control group of 113 adolescents (47.8% girls), aged between 11 and 18 years old, from the UP & DOWN study were included in this substudy. Serum C-reactive protein, C3 and C4 complement factors, total proteins, interleukin-6, tumour necrosis factor-alpha, insulin, cortisol, leptin, adiponectin, galactin-3 and visfatin were analysed; homeostatic model assessment index was calculated. In order to evaluate adiposity, we measured the following body fat variables: weight, height, waist circumference and skinfold thicknesses. Birth weight was obtained by questionnaire. In addition, body mass index, waist-to-height ratio (WHtR) and body fat percentage (BF%) were calculated. Results Down syndrome group showed higher levels of body mass index, WHtR, waist circumference, BF% and lower birth weight than controls (P < 0.001). In the general linear model in the total sample, WHtR was positively associated with C3 and C4 (P < 0.001) as well as with leptin levels (P = 0.015). BF% was positively associated with total proteins (P = 0.093) and leptin levels (P < 0.001). DS was positively associated with total proteins (P < 0.001), C3 (P = 0.047) and C4 (P = 0.019). Despite the higher levels of adiposity found in DS group, no direct association was found between BF% and leptin levels, comparing with the control group. Conclusions These findings suggest that abdominal obesity should be controlled in adolescents because of its relationship with acute phase-inflammatory biomarkers but especially in DS adolescents who may show a peculiar metabolic status according to their relationship between adiposity and inflammatory biomarkers.