BACKGROUND: Soybean oligosaccharides (SBOSs) are potential prebiotics that may be used to improve immune function. Here, we investigated the effects of intragastric administration of SBOSs in mice to determine the effects on autochthonous intestinal microbial communities and immunological parameters. RESULTS: After 22-day administration, 4.0 g·kg body weight (BW)-1 SBOSs significantly enhanced the proliferation of bifidobacteria and lactic acid bacteria (LAB) as compared to the control. This dose of SBOSs also significantly increased numbers of enterococci and decreased numbers of Clostridium perfringens. Treatment with 4.0 g·kg BW-1 SBOSs also significantly increased the percentage of T-lymphocytes and lymphocyte proliferation as compared to the control, suggesting that SBOSs promoted cellular immunity in mice. Additionally, 4.0 g·kg BW-1 SBOSs induced significant differences in hemolysin production, natural killer (NK) cell activity, phagocytic activity, cytokine production, and immunoglobulin levels compared to the control. CONCLUSION: Our data demonstrated that intragastric administration of SBOSs at a dose of 4.0 g·kg BW-1 improved the numbers of beneficial intestinal microbes and enhanced immunological function of mice.