Synbiotic supplements, which contain multiple functional ingredients, may enhance the immune system more than the use of individual ingredients alone. A double blind active controlled parallel trial over a 21 d exercise training period was conducted to evaluate the effect of Gut Balance™, which contains Lactobacillus paracasei subsp. paracasei (L. casei 431®), Bifidobacterium animalis ssp. lactis (BB-12®), Lactobacillus acidophilus (LA-5®), Lactobacillus rhamnosus (LGG®), two prebiotics (raftiline and raftilose) and bovine whey derived lactoferrin and immunoglobulins with acacia gum on fecal microbiota, short chain fatty acids (SCFA), gut permeability, salivary lactoferrin and serum cytokines. All subjects randomized were included in the analysis. There was a 9-fold (1.2-fold to 64-fold; 95% confidence intervals p = 0.03) greater increase in fecal L. paracasei numbers with Gut Balance™ compared with acacia gum supplementation. Gut Balance™ was associated with a 50% (-12% to 72%; p = 0.02) smaller increase in the concentration of serum IL-16 in comparison to acacia gum from pre- to post-study. No substantial effects of either supplement were evident in fecal SCFA concentrations, measures of mucosal immunity or GI permeability. Clinical studies are now required to determine whether Gut Balance™ may exert beneficial GI health effects by increasing the recovery of fecal L. paracasei. Both supplements had little effect on immunity. Twenty two healthy physically active male subjects (mean age = 33.9 ± 6.5y) were randomly allocated to either daily prebiotic or synbiotic supplementation for 21 d. Saliva, blood, urine and fecal samples were collected pre-, mid and post-intervention. Participants recorded patterns of physical activity on a self-reported questionnaire.