Carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) regulates intestinal immunological homeostasis. However, precise expression patterns of CEACAM1 isoforms remain poorly understood in the intestinal epithelia. Focusing on the small intestinal epithelium of BALB/c mice, we identified three novel splice variants encoding CEACAM1(a)-2, -2C1, and -4C1 by RT-PCR. CEACAM1(a)-2, -2C1, and -4C1 demonstrated secretory properties by transfection experiments in vitro. Among them, CEACAM1(a)-4C1 was the major secreted isoform in vivo due to the soluble/secreted CEACAM1(a) with a frameshift sequence in the C-terminus, specific for CEACAM1(a)-2C1 and -4C1. CEACAM1(a)-4C1 was capable of binding murine hepatitis virus (MHV) and was detected at approximately 120kDa in the small intestinal secretions. Neutralizing effects of the soluble CEACAM1(a) on MHV infectivity in vitro were demonstrated by using recombinant CEACAM1(a)-4C1. Our data suggest an intrinsic mechanism operated by free CEACAM1 for surveillance of pathogens and maintenance of homeostasis in the intestine.