The study aimed at determining the effect of inulin and/or a multispecies probiotic formulation on gastrointestinal tract (GIT) morphology, immunological and haematological parameters. Forty-eight newly weaned piglets were assigned to four feeding groups, receiving a standard basal diet (control), supplemented with 0.4% inulin, probiotics (1 x 10(9) CFU/kg as fed, enterococci, lactobacilli, bifidobacteria) or a combination of both (synbiotic). After four weeks of ad libitum feeding piglets were slaughtered and intestinal tissue samples were obtained for histometry. Additional tissue samples of the GIT, mesenteric lymph nodes, blood, liver and spleen were taken for mRNA expression analysis of cell turnover (CDK4, caspase3, IGF I), transcription factor NFkappaB and inflammatory marker genes (TNFalpha, TGFbeta). Changes in histometry occurred predominantly in the small intestine, showing higher jejunal villi when probiotics were administered alone (p < 0.10). Inulin decreased the number of acidic goblet cells in jejunal villi (p < 0.05), whereas probiotics increased neutral goblet cells in ileal villi (p < 0.05). Though inflammatory marker genes were uninfluenced by treatment in the proximal GIT, the colon showed downregulations induced by inulin (TNFalpha: p < 0.10, TGFbeta: p < 0.05). Gene expression of CDK4 was upregulated in the jejunum and of TGFbeta in the mesenteric lymph nodes in the probiotic groups. Interestingly, the probiotic group alone exhibited upregulations in cell turnover marker genes in the colon and blood. Furthermore, for numerous parameters, inulin and probiotics led to no synergistic but antagonistic interactions.