Inflammation markers (IM) have been associated with the development of chronic diseases. This study compares the effects on IM of three exercise programs combined with a hypocaloric diet.119 overweight participants (73 women, 46 men) aged 18-50 years were randomised into four treatment groups: strength training (S; n = 30), endurance training (E; n = 30), combined S + E (SE; n = 30), and a diet and physical activity recommendations group (D; n = 29). Energy intake, anthropometric variables (AV), training variables (VO2peak, strength index, dynamometric strength index [DSI]) and plasma IM were recorded at baseline and after 22 weeks of treatment.84 participants completed the study. At 22 weeks, all groups showed a significantly reduced energy intake (P < 0.001) and improved AV (P < 0.001). VO2peak significantly increased in all groups (P < 0.01). DSI increased in the exercise groups only (P < 0.05). Plasma leptin fell significantly (P < 0.001) in the S and E groups, but not significantly in the SE group (P = 0.029) (no significant differences between these groups). Tumour necrosis factor-α (TNF-α), and C-reactive protein (CRP) concentrations decreased in all groups when examined together, but not when examined separately. No significant differences were seen in interleukin-6 (IL-6).Combining strength or endurance training with a hypocaloric diet improved AV and reduced plasma leptin concentrations. No differences were seen between groups in terms of TNF-α, IL-6 or CRP reduction. This trial was registered at clinical trials.gov as NCT01116856. http://clinicaltrials.gov/.