Giardia lamblia is a flagellated protozoan that causes watery diarrhea worldwide but the mechanisms of pathogenicity and the major host defenses against Giardia infection are not well characterized. The recent sequencing of the G. lamblia genome and the development of methods for genome-wide analyses of gene expression have made it possible to characterize the host-parasite interaction more fully. It is becoming clear that the host defense against a Giardia infection involves several different immunological and non-immunological mucosal processes.