A Density Functional calculation is performed to analyze the PTCDA/Au(111) interface, including the effect of the molecular charging energy on the transport gap. The calculated transport gap is 2.9 eV, and the lowest unoccupied molecular orbital, or LUMO, level is found at 4.25 eV below the vacuum level. We show that the alignment between the metal and the organic levels is controlled by the charge transfer between the two materials, as determined by the difference between the molecule Charge Neutrality Level, or CNL, (located 0.3 eV below the LUMO level) and the metal work function. We compare with inde-pendent General Gradient Approximation–Density Functional calculations, DFT–GGA, yielding an energy gap of 1.4 eV; we find, however, good agreement between both approaches for the CNL and the interface potential step. Good agreement is also found between our results and the experimental evidence.