In this work, an atomic force microscope (AFM) with an integrated thermal sensor has been used to obtain the local spatial distribution of temperatures in a micromachined thermopile with submicron resolution. In this communication, we will show how the dimensional, structural and functional characteristics of a thermopile suits well with the requirements for AFM thermal imaging, and how a deeper insight of the thermopile operation can be gained with the aid of these advanced scanning probe-based tools.