Prebiotics may increase Zn absorption, a mineral known to play a central role in the immune system. Zn-deficient states are characterised by suppressed immune function, while prebiotics may improve both gut and cell-mediated immunity. Our objective was to determine if inulin alters the number and proportion of immune cells in the spleen, mesenteric lymph nodes (MLN) and Peyer's patches (PP), ex vivo cytokine secretion, intestinal permeability and Zn status in healthy as well as Zn-deficient rats. Weanling female rats were fed diets supplemented with 5 % cellulose (CEL) or 5 % inulin (PRE) for 4 weeks. The rats received the CEL or PRE diet ad libitum (ZN) or in restricted amounts (DR), or deficient in Zn (ZD) for another 4 weeks. The PRE-fed rats had a higher number and proportion of dendritic cells in PP, and greater ex vivo secretion of IL-2, IL-10 and interferon-γ from spleen and MLN cells compared with CEL-fed rats. PRE reduced the number and proportion of T cell receptor (TCR)-αβ+CD8+ cells in spleen and CD45RA+ cells in MLN compared with CEL. ZD rats had lower serum IgG2a and T cell numbers in MLN compared with ZN and DR rats. TCRγδ+ cell numbers in PP were higher in ZD-PRE rats compared with ZD-CEL rats. Femur Zn concentrations of DR-PRE rats were higher than those of DR-CEL rats. Intestinal permeability was unchanged. The higher proportion and number of dendritic cells in the PP of inulin-fed rats indicates a need for further research on how prebiotics and their metabolites affect immune function possibly through intestinal dendritic cells.