In this study, the fully developed, steady, laminar flow of blood is studied in a long pipe with square and circular cross-sections subjected to a magnetic field generated by an electric wire. Temperature difference between the walls causes heat transfer within the fluid by the displacement of the magnetizable fluid particles in the cavity. The governing equations are the coupled Navier-Stokes and energy equations including magnetization terms. The axial velocity is also computed with the obtained plane velocity. The Dual Reciprocity Boundary Element Method (DRBEM) is used by taking all the terms other than Laplacian as inhomogeneity which transforms the partial differential equations into the boundary integral equations. Numerical results are given for increasing values of Magnetic (Mn) and Rayleigh (Ra) numbers. The numerical results reveal that an increase in Mn accelerates the plane velocity in the cavity but decelerates the axial velocity around the magnetic source. Pressure increases through the channel starting from the magnetic source. Isotherms show the cooling of the channel with high Mn and Ra only leaving a thin hot layer near the top heated wall. As Ra increases viscous effect is reduced leaving its place to convection in the channel. The use of DRBEM has considerably small computational expense compared to domain type methods.