In order to identify potential unanticipated side reactions and immune responses, the evaluation of candidate vaccines should include immunization of the murine model of the disease in question and mutant animals, as well as normal laboratory animals. We employed WBB6F1-W/Wv and WBB6F1-Sl/Sld mutant mice, which are genetically mast cell deficient and lack intestinal pacemaker activity due to a severe deficiency in interstitial cells of Cajal. Antigen-specific mucosal and systemic immune responses in the mutant and congenic normal mice were induced by intranasal or intragastric immunization with ovalbumin (OVA) plus cholera toxin as an adjuvant. It was found that the levels of the OVA-specific humoral immune response in the mucosal and systemic tissues of the mutant mice immunized intranasally were roughly equivalent to those of the congenic normal mice. In contrast, the specific humoral immune response in the intragastrically immunized mutant mice was greater than that observed in the congenic normal mice. Unexpectedly, the titers of OVA-specific IgA antibodies and total IgA antibodies in the fecal extracts of both intranasally and intragastrically immunized mutant mice were significantly lower than in those of the congenic normal mice. Although the detailed mechanisms leading to these differences remain unclear, the unexpected immune responses observed in the gastrointestinal tracts of the mice in this study may be related to an abnormality of gastrointestinal motility. Our data therefore suggest that studies using mutant mice and physiological assessments should be carried out during mucosal vaccine development.