The natural defense systems of animals, including humans, have been developed to maintain the hosts' health by fighting exogenous microbes. Immune systems, which have functions to recognize and keep out exogenous organisms, play a central role in the host defense systems. Intestinal microflora, mainly composed of commensal bacteria, also provide defense functions called colonization resistance to keep out exogenous bacteria. We have been investigating probiotic strains Lactobacillus johnsonii La1 (NCC533) and Bifidobacterium animalis subspp. lactis Bb-12 to elucidate the efficacy of these probiotic strains in strengthening the natural defense system of the host and their potential for risk reduction of infections as an end point benefit. Feeding trials using fermented milk with L. johnsonii La1 (LC1 ® ) showed that intestinal microflora were improved and blood phagocytic activity, a biomarker for natural immunity, increased in healthy adults. In a feeding trial of LC1 in the elderly, we found that the frequency of infection was reduced by administration of the probiotics. In the LC1-fed elderly, blood phagocytic activity increased, and serum TNF-α, an inflammation biomarker, was lowered. Serum albumin, a biomarker for nutritional status, also increased in the LC1-fed elderly, suggesting that probiotic feeding may contribute to regulation of infection through immune system modulation, activation of immunity and suppression of inflammation, and nutritional status improvement. The La1 strain was shown to stimulate the parasympathetic nerve system in vivo, implying that anabolic action might contribute to nutritional status improvement. An anti-inflammatory effect of the La1 strain was also observed in the animal studies using colitis, Helicobacter pylori-infection, and atopic dermatitis models, and a human study in pollen allergy patients. Feeding of the Bb-12 strain in weaning children improved intestinal microflora and increased intestinal IgA production. Probiotics such as L. johnsonii La1 and Bifidobacterium Bb-12 could play a significant role in improving the QOL of human beings through strengthening the natural defense systems of the host. In this paper, we review and discuss our recent work with references to other research.