Heat is a familiar form of energy transported from a hot side to a colder side of an object, but not a notion associated with microscopic measurements of electronic properties. A temperature difference within a material causes charge carriers, electrons or holes to diffuse along the temperature gradient inducing a thermoelectric voltage. Here we show that local thermoelectric measurements can yield high-sensitivity imaging of structural disorder on the atomic and nanometre scales. The thermopower measurement acts to amplify the variations in the local density of states at the Fermi level, giving high differential contrast in thermoelectric signals. Using this imaging technique, we uncovered point defects in the first layer of epitaxial graphene, which generate soliton-like domain-wall line patterns separating regions of the different interlayer stacking of the second graphene layer.