This study demonstrated that oral feeding of heat-inactivated Lactobacillus (L b.) kefiranofaciens M1 from kefir grains effectively inhibited immunoglobulin (Ig) E production in response to ovalbumin (OVA) in vivo. The pattern of cytokine production by splenocyte cells revealed that the levels of cytokines produced by T helper (Th) 1 cells increased, and those of cytokines produced by Th2 cells decreased in the heat-inactivated M1 feeding group. These findings indicated that Lactobacillus kefiranofaciens M1 in the kefir played an important role in antiallergic activities. By additional analysis using flow cytometry and microarray, the mechanism of suppression of IgE production by oral feeding of the heat-inactivated M1 probably occurs because of upregulation of the expression of Cd2, Stat4, and Ifnr leading to skewing the Th1/Th2 balance toward Th1 dominance, elevation of the CD4(+)CD25(+) regulatory T (Treg) percentage, and reduction of activated CD19(+) B cells. Downregulation of complement system and components was also involved in suppression of IgE production. Practical Application: Kefir has long been considered good for health. Its health benefits include immunoregulatory effects. However, there is a lack of knowledge concerning the immunoregulatory effects induced by kefir lactic acid bacteria (LAB). Our data clearly demonstrated the antiallergic activity of kefir LAB, Lactobacillus (L b.) kefiranofaciens M1. By additional analysis using flow cytometry and microarray, the possible mechanism of suppression of IgE production by oral feeding of the heat-inactivated M1 was also elucidated. Our findings indicated that Lactobacillus kefiranofaciens M1 may have a great potential for utilization in functional food products.