Background During the course of infection with the protozoan parasite Giardia duodenalis, both mucus production and structure of the mucus layers have been shown to be altered throughout the large and small intestines. This potentially has significant impacts on mucosal barrier function, predisposing a host to mucosal inflammation, which contributes both to Giardia pathogenesis and to development of post-infectious complications. We have attempted to characterize the mechanisms by which Giardia modulates mucus production and secretion by intestinal goblet cells, as well as chemical alterations to mucin proteins that occur in response to Giardia infection. Several effects have been found to be dependent on Giardia cysteine protease activity, suggesting a potential mechanism involving protease activated receptors. Methods The human colonic epithelial cell line LS174T was infected with Giardia trophozoites (isolates NF, WB, S2, and GSM). Prior to infection, trophozoites were treated with E64, a broad-spectrum cysteine protease inhibitor, and LS174T were treated with a pepducin PAR2 antagonist, BAPTA, a calcium chelator, or U0126, an ERK1/2 inhibitor. MUC2 mucin gene expression was assessed using quantitative PCR (qPCR). Wild type (WT) and PAR2 deficient (PAR2 −/−) mice were infected with Giardia trophozoites. The colonic mucus layer was stained using WGA and qPCR was performed for Muc2 and Muc5ac in the small and large intestines. Expression of glycosyltransferase enzymes was assessed using qPCR. Results Giardia NF, S2, and WB, but not GSM, upregulate MUC2 expression in LS174T cells. This increase was attenuated by inhibition of Giardia cysteine proteases and by antagonism of PAR2 or inhibition of calcium release or ERK1/2 signaling in LS174T cells. Giardia infected WT mice show increased Muc2 and Muc5ac expression in the colon, and increased Muc5ac but decreased Muc2 expression in the jejunum. These changes were not seen in PAR2−/− mice. Both WT infected and PAR2−/− non-infected mice showed thinning of the colonic mucus layer compared to WT controls. There was some recovery in thickness in PAR2−/− infected mice. Expression of the fucosyltransferase Fut2 was increased in the jejunums of WT mice, while the sulfotransferase Chst4 was decreased. Expression of the glycan core synthase C2GnT1 was increased in the WT jejunum, while C1GalT1 expression was slightly decreased in the jejunum and colon. Conclusions Giardia-induced alterations to mucin gene expression in vitro and in vivo are dependent on PAR2 signaling. Canonical PAR2 signaling, characterized by calcium release and ERK1/2 pathway activation, contribute to altered expression of the MUC2 mucin in colonic goblet cell cultures. Expression of several glycosyltransferases, responsible for the addition of glycan groups to intestinal mucins, are altered during Giardia infection in vivo, suggesting mucosal alterations may involve chemical modifications of mucin proteins.