The effects of various dietary fibres on gut health have been studied extensively but their combined effects are scarcely documented. In the present study the effects of 2 % (w/w) polydextrose (PDX), 2 % (w/w) disaccharide lactitol, or 2 % (w/w) PDX+2 % (w/w) lactitol on gut microflora, microbial metabolism and gut immune responses were investigated in rats. Both PDX and lactitol alone had an effect on many of the studied parameters, but their combination had stronger than additive effects in some parameters. The PDX+lactitol combination altered the microbial community structure as seen by a culture-independent method, percentage guanine+cytosine (%G+C) profiling, increasing the areas of %G+C 35-39 (P<0.0001) and %G+C 45-49 (P=0.0002), and decreasing %G+C 65-74 (P<0.0003). These changes were also reflected in the microbial metabolism so that the production of biogenic amines and branched volatile fatty acids was significantly reduced, by 12 (P=0.03) and 50 % (P=0.002), respectively, indicating a shift from putrefactive towards saccharolytic metabolism. PDX increased the secretion of IgA in the caecum (P=0.007). Secretion of IgA increased even more, almost ten-fold, with the combination of PDX+lactitol (P<0.0001) when compared with the control group. Lactitol increased the production of butyrate by caecal microbes by two- to three-fold when compared with the PDX or control group (P<0.0001). Butyrate is a preferred energy source for mucosal cells; thus a boost in the availability of energy for immune cells may have still added to the synergistic effects of PDX and lactitol on immune cells. It is noteworthy that improvement in the IgA secretion occurred without signs of mucosal inflammation.