Factor B is an essential component of the complement cascade which forms the C3 and C5 convertase of the alternative pathway. Factor B cleavage products also function as cofactors in antibody-independent monocyte-mediated cytotoxicity, macrophage spreading, plasminogen activation and proliferation of B lymphocytes. Several healthy kindreds heterozygous for the factor B null or non-functional allele have been reported but the absence of homozygous factor B deficiency in humans or in animals has been speculated to be caused by the lethality of the phenotype. Here we report the generation of factor B-deficient mice by gene targeting in vivo. These mice were born at the expected Mendelian ratio and they both develop and breed normally in a conventional animal facility. These mice represent a model of complete alternative pathway deficiency. This model enables the dissection of the complement cascade in vivo and the elucidation of the relative contribution of this complement pathway in the various physiological and pathological phenomena ascribed to the complement system.