It is presented in this work a general numerical tool for the analysis of three-dimensional bimaterial interface cracks. The proposed tool is based on a multidomain formulation of the Boundary Element Method (BEM), with the crack located at the interface. Mixed-mode stress intensity factors along three-dimensional bimaterial interface cracks are computed using M1-Integral methodology, which imposes the asymptotic auxiliary fields for the plane problem of a bimaterial interface crack along the crack front. The M1-integral is evaluated using a domain representation naturally compatible with the BEM, since stresses, strains and derivatives of displacements at internal points can be evaluated using the appropriate boundary integral equations. The capability of the procedure is demonstrated by solving an application example, namely the analysis of a fibre/matrix debond interface crack under transverse loading.