Methods and structures for thermoelectric cooling of 3D semiconductor structures are disclosed. Thermoelectric vias (TEVs) to form a thermoelectric cooling structure. The TEVs are formed with an etch process similar to that used in forming electrically active through-silicon vias (TSVs). However, the etched cavities are filled with materials that exhibit the thermoelectric effect, instead of a conductive metal as with a traditional electrically active TSV. The thermoelectric materials are arranged such that when a voltage is applied to them, the thermoelectric cooling structure carries heat away from the interior of the structure from the junction where the thermoelectric materials are electrically connected.