It is well established that mast cells are important effector cells mediating the acute phase of IgE-associated allergic disorders, but their roles in late phase reactions and chronic allergic inflammation are not well defined. Here we describe an experimental approach for analyzing mast cell functions in vivo by comparing the biological responses in wild-type mice, genetically mast cell-deficient mice, and 'mast cell knock-in mice' (mast cell-deficient mice selectively repaired of their mast cell deficiency). Studies using 'mast cell knock-in mice' have indicated that mast cells can contribute importantly to IgE-associated late phase reactions and to chronic allergic inflammation. Moreover, 'mast cell knock-in mice' containing adoptive-transferred mast cell populations with defined alterations in the expression of specific mast cell products can be used to characterize the mechanisms by which mast cells contribute to the expression of the response of interest.