Coeliac disease (CD), an inflammatory enteropathy, is believed to be caused by immune sensitivity to ingested gluten. T-cell activation appears to be implicated in the disease although little is known regarding the role of T-cell subsets, Th1/Th2, and the cytokines they secrete. Reverse transcription-polymerase chain reaction was used to examine the mRNA expression of a wide profile of cytokines in intestinal and peripheral samples taken from active and inactive CD paediatric patients. Differential mRNA expression was observed for cytokines, between CD patients and controls, in both compartments. The percentage of samples expressing interleukin (IL)-2, interferon (IFN)-gamma, tumor necrosis factor (TNF)-beta, IL-10, IL-1beta, TNF-alpha and transforming growth factor (TGF)-beta mRNA from active CD patients was higher than from controls. A prominent finding was the expression of both Th1 (IFN-gamma, IL-2) and Th2 (IL-4, IL-10)-associated cytokine transcripts in the same biopsies and peripheral blood cells from patients with active CD implying activation of Th0 cells. The expression of IL-2 and IL-4 mRNA was not observed in peripheral blood samples from inactive CD patients associating them with disease activity. These results are important to the understanding of the inflammatory process in CD while cytokine levels may prove to be relevant markers of disease activity.