It is difficult to distinguish clinically between bacterial and viral causes of enterocolitis. The aim of the study was to investigate if serum cytokines can distinguish bacterial from viral enterocolitis. We prospectively enrolled 147 paediatric in-patients with acute enterocolitis. Blood was taken for leucocyte count, CRP, ESR, IL-6, IL-8, IFN-alpha and TNF-alpha on the day of admission. A pathogen was identified in 115 of the 147 children, 72 of whom had a bacterial pathogen (bacterial group) and 43 rotavirus (viral group). Mean values of the serum markers IL-6, IL-8 and CRP were significantly higher in the bacterial group. Receiver-operating characteristic curves demonstrated that a cut-off of 15 pg/ml for IL-6 had a sensitivity of 0.75 and a specificity of 0.91 for bacterial diarrhoea. Comparable values for CRP at a cut-off of 13 mg/L demonstrated a sensitivity of 0.54 and a specificity of 0.72. Values for IL-8 at a cut-off of 80 pg/ml had a sensitivity of 0.46 and a specificity of 0.71. Despite the small sample size, our data suggest that serum IL-6, IL-8 and CRP are significantly elevated in children with bacterial enterocolitis. IL-6 has a higher sensitivity, specificity and positive predictive value than IL-8 and CRP. Determination of serum cytokines might be a useful way of differentiating viral from bacterial gastro-enteritis.