During the course of a giardial infection, the host’s immune system is presented with a variety of Giardia antigens as trophozoites differentiate, through encysting cells, to form the infective cysts. Previous studies examining the host’s immune response during giardial infections have focused on trophozoite-derived antigens (Ags). In this study, we were interested to determine if the host’s immune system reacts to cyst Ags during the acute and elimination phases, when there is cyst shedding. For this purpose, we used antigenic extracts from trophozoites (Troph), encysting cells (ENC), and purified giardial cyst walls (PCW), as well as purified recombinant cyst wall protein 2 (rCWP2). Comparative analysis of the parasite extracts using SDS–PAGE analysis and surface-enhanced laser desorption/ionization time of flight mass spectrometry resulted in the detection of 175 protein entities, of which 26 were Troph-specific proteins, 17 ENC-specific proteins, and 31 were PCW-specific proteins. On the other hand, we detected 34 proteins shared between Troph and ENC, 19 proteins that were shared between ENC and PCW, and 29 proteins that were common to Troph and PCW. Finally, we detected 19 proteins that were shared by all three extract samples. BALB/c mice were infected with 105Giardia muris cysts and sacrificed either at the acute or elimination phases of infection (days 12 and 40, respectively), and lymphocytes were isolated from the Peyer’s patches (PP). Using flow cytometry, we detected significant increases in the number of PP-derived CD4+ and CD19+, but not CD8+ lymphocytes. Quantification of the number of mucosal IL-4 and IFN-γ secreting T-lymphocytes by enzyme-linked immunosorbent spot assay showed that these cells reacted by secreting similar levels of IL-4 and IFN-γ, regardless of the Ag or the phase of infection. Analysis of intestinal humoral immune responses by ELISA resulted in the detection of Ag-specific IgA and IgG intestinal antibodies. Regardless of the Ag tested, a trend was consistently observed where the concentration of local antibodies was found to be slightly increased by the acute phase, where we detected ∼200μg/mg of specific IgA and ∼300ng/ml of specific IgG in intestinal lavage of infected mice. By the elimination phase, the amount of specific antibodies was found to increase to ∼600μg/mg of specific IgA and ∼1300ng/ml of specific IgG antibodies. Finally, we tested the biological activity of these antibodies and found that they were able to reduce the ability of trophozoites to differentiate into cysts in vitro. Collectively, we believe these results demonstrate for the first time the existence of significant cellular and humoral immune responses against Giardia cyst Ags that may contribute to the reduction of cyst shedding in infected animals.