The parasitic protozoan Giardia lamblia is a worldwide cause of diarrhea, but the mechanism of disease remains elusive. The parasite colonizes the small intestinal epithelium, known to be a sensor for the presence of enteric pathogens, without invading or causing severe inflammation. In this study we investigated the epithelial cell response to G. lamblia. Differentiated Caco-2 cells were infected with G. lamblia isolate WB-A11, and the transcriptome of the intestinal cells was analyzed after 1.5, 6, and 18 h of interaction, using oligonucleotide microarrays. A large number of genes displayed changed expression patterns, showing the complexity of the interaction between G. lamblia and intestinal cells. A novel chemokine profile (CCL2, CCL20, CXCL1, CXCL2, and CXCL3) was induced that was different from the response induced by enteric pathogens causing intestinal inflammation. Several genes involved in stress regulation changed their expression. These findings indicate that the intestinal epithelium senses the G. lamblia infection, and this is important for induction of innate and adaptive immunity. The induced stress response can be important in the pathogenesis.