Transparent conducting oxides have been previously investigated for both bulk and thin film thermoelectric applications, and have shown promising results due to their thermal stability and electrical conductivity. Alloys of two or more transparent conducting oxides have been deposited using pulsed laser deposition (PLD) and combinatorial sputtering, and the resulting films were optimized for optical applications. In this study, thermoelectric materials were prepared by co-sputtering techniques, whereby a chemical gradient was formed across an alumina substrate that was patterned using photolithography to form hundreds of micro-thermocouples. The systems indium tin oxide (ITO), indium zinc oxide (IZO), and zinc tin oxide (ZTO) were investigated for this purpose and the resulting combinatorial libraries were rapidly screened to establish room temperature resistivity, Seebeck coefficient, and power factor as functions of both composition and heat treatment, in nitrogen and air ambients. Due to their chemical stability, oxidation resistance, and large Seebeck coefficients relative to metal thermocouples, these materials are ideal for temperature measurement or energy harvesting in harsh environments such as gas turbine engines.