The stability analysis of laminar channel flow subject to spanwise thermal modulations is presented. Modulations create streamwise streaks and rolls, producing three-dimensional flow structures. It is shown that these structures induce a new type of instability which persists at low Reynolds numbers. Detailed characterization and quantification of this instability are given, including an explanation of its mechanism. It is shown that heating intensity and spatial distribution control this instability; its intensity increases with a reduction of the Prandtl number, and it can be induced by heating of either wall.