Background: The resident host microflora condition and prime the immune system. However, systemic and mucosal immune responses to bacteria may be divergent. Thus, in vitro models using cells derived from the systemic immune system may not accurately reflect the response of mucosal cells. Aim: To compare, in vitro, cytokine production by mesenteric lymph node cells (MLNCs), mesenteric lymph node derived dendritic cells and peripheral blood mononuclear cells (PBMCs) to defined microbial stimuli. Methods: Fresh mesenteric lymph nodes were obtained from IBD patients following colon resection (n=10). Peripheral blood was isolated from a separate group of IBD patients (n=12). The mononuclear cell populations were isolated using Ficoll-histopaque density centrifugation. MLN derived dendritic cells were isolated by negative selection (i.e. T cells, B cells and progenitor cells were removed by antibody labelling and magnetic separation). Isolated cells (purity >95%) were incubated in vitro for 72 hours with the probiotic bacteria, Lactobacillus salivarius or Bifidobacterium infantis, or the pathogenic organism Salmonella typhimurium. IL-12, TNF-a and IL-10 cytokine levels were quantified by ELISA. Results: PBMCs secreted TNFa in response to the lactobacillus, bifidobacteria and salmonella strains, while MLNCs and MLN derived dendritic cells secreted TNFa only in response to salmonella challenge. PBMCs secreted IL-12 following co-incubation with salmonella or lactobacilli, while MLNCs and MLN derived dendritic cells produced IL-12 only in response to salmonella. PBMCs secreted IL-10 in response to the bifidobacteria cells, but not in response to the lactobacillus or salmonella strain. However, MLNC and dendritic cells secreted IL-10 in response to bifidobacteria and lactobacilli, but not in response to salmonella. Conclusion: Stain-strain divergence in cytokine responses (i.e. commensal versus pathogen) are more marked in cells isolated from the mucosal immune system compared to peripheral blood mononuclear cells. Caution must be exercised when extrapolating biological significance from different in vitro models as cells isolated from different sites will yield variable results..