A cross-sectional study was carried out in order to compare intestinal microbiological and immunological biomarkers with blood glucose and lipids, satiety-related hormones and inflammatory biomarkers characterising differences between obese and normal weight subjects. Faecal and blood samples were obtained from twenty obese subjects with an average BMI of 32.9 kg/m2 and twenty normal weight subjects with an average BMI of 23.3 kg/m2. Blood insulin, TAG and leptin were significantly elevated, whereas concentrations of HDL and ghrelin were significantly decreased in the obese subjects. Inflammatory status in the obese subjects was characterised by a trend for elevated blood C-reactive protein (CRP; P = 0.06) and IL-6 (P = 0.02). The faecal microbial composition differed between the groups; less sulphate-reducing bacteria (P = 0.05) and a trend for less Bacteroides (P = 0.07) were measured for overweight subjects. Furthermore, an inverse correlation was demonstrated between faecal Bacteroides levels and waist circumference (P = 0.05). The faecal microbial metabolites differed between the groups; increased concentrations of branched-chain fatty acids, phenolics, valeric acid, di- and hydroxy acids were described in the obese subjects. No differences between the measured intestinal inflammatory biomarkers were detected. However, systemic inflammation (CRP and IL-6) was correlated with the faecal concentrations of phenolics and lactic acid (P < 0.05 and 0.05, and P < 0.01 and 0.05, respectively). In summary, weight-related differences were observed both in the intestinal microbial composition and its activity. The role of intestinal signals, such as phenolics and lactic acid in the development of weight-related problems, needs to be studied further.