Over the past decades, research on in vivo functions of mast cells has largely relied on kit-mutant mouse strains. Recently, new mouse models for investigation of mast cell functions based on the Cre/loxP recombination system have been published and results in these new models challenged findings of previous studies in kit-mutant mice. Herein we describe procedures central to mast cell-specific gene inactivation and the generation of mast cell-deficient mice based on the mouse strain Mcpt5-Cre, which expresses Cre recombinase selectively in connective tissue mast cells.