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We use conducting atomic force microscopy (AFM) in ultra high vacuum to measure the thermoelectric power of Au, Pt, and 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) films. Tips coated with thick (1200 nm) Pt films or highly doped diamond film give reproducible data. The thermoelectric power of metal junctions formed with diamond tips is high but dominated by the diamond material thus making diamond tips of limited applicability in thermovoltage AFM. Pt coated tips on Au or Pt films gives small thermovoltage signal, making quantitative analysis of the thermopower on metal sample problematic. The thermovoltage AFM technique appears best suited to study organic thin films and the thermoelectric power of 1.5 nm and 2 nm thick PTCDA deposited on Au measured with Pt tips is -342 and -372 μV/K, respectively. The negative sign indicates that the lowest unoccupied molecular orbital level dominates electrical transport.