In this paper a boundary element formulation for heat conduction problems are presented. The different types of boundary conditions of conduction, convection and radiation are included in the integral equations. The transient fundamental solution is used and by considering small time limits the integration over the time domain are calculated analytically. In the absence of a radiation boundary condition a set of linear system of equations would be developed. While, in the presence of radiation boundary conditions, a set of nonlinear system of equations is resulted. Also presented in this paper a multi-region boundary element analysis for heat conduction problems composed of different materials having different thermal properties. The compatibility and equilibrium are used to link the systems of equations developed for each region. Examples are provided to check the accuracy of the method and the implementation.