During the last years, an antimicrobial protein from the RegIII family has been consistently identified as one of the main up-regulated mRNA transcripts in the pig small intestinal mucosa during different infections such as enterotoxigenic Escherichia coli (ETEC). This transcript has been mainly referred to in the literature as pancreatitis-associated protein (PAP/RegIIIα). However, the identity of this transcript has not been confirmed, and no evidence of its expression at the protein level is available in the literature, because the absence of a specific antibody. In this study, we first unequivocally identified the PAP/RegIII family protein mainly expressed in ETEC infected pig intestine as RegIIIγ by 2D-DIGE and MALDI-TOF/TOF. This shows that the pig differs from species like human and mice in that RegIIIγ (and not RegIIIα) might be the major RegIII isotype during intestinal infection. Immunoblotting analysis with a specifically generated polyclonal rabbit antibody revealed that pig RegIIIγ is expressed throughout the intestinal tract, but most abundantly in the ileum. Although a higher abundance of mRNA was paralleled by higher protein abundance, a lack of linear relationship was found between RegIIIγ mRNA and protein abundances in the jejunal mucosa, the latter most pronounced in the case of natural infection. This may be related to the secretory nature of RegIIIγ. This would mean that the antimicrobial protein RegIIIγ is a good candidate as a non-invasive faecal intestinal health biomarker in swine.