Purpose – The purpose of this paper is to present a 3D model of deep welding of dissimilar metals and to show how to model the electron beam deflection due to thermoelectric fields caused by temperature gradients in some dissimilar metals (Seebeck effect). Design/methodology/approach – A 3D thermoelectric and heat conduction model is used to estimate the deflection of the electron beam used during welding of dissimilar metals. A weak coupling between analysed fields is assembled. Additionally, the influence of the deflection on the calculated fields was not taken into account. The problem is solved using a finite element method. Findings – It is possible to model Seebeck effect in a relative simple way using the finite element approach. Originality/value – The paper presents a detailed description of modelling procedure of a complex coupled field problem.