The chemical structure, including changes in charge distribution upon doping, for vapor-deposited polythiophene films has been investigated using x-ray photoelectron spectroscopy (XPS). Two different methods of doping, coevaporation with FeCl3 and exposure to iodine vapor, are contrasted in this study and several chemical states are observed for the "dopants" associated with these complexes. In general, the FeCl3 codeposited complexes have considerably higher conductivities than the iodine exposed films (10-25 S/cm as compared to 0.01 S/cm). Furthermore, besides being a more effective doping mechanism, the FeCl3 codeposited complexes are much more stable upon exposure to atmosphere and also in the ultrahigh vacuum environment of the XPS system. Atomic force microscopy images of the same films show clear morphological differences between the as-deposited, the FeCl3 codeposited, and the iodine doped films. The as-deposited film shows a fibrillar-type structure while the FeCl3 codeposited film is observed to coalesce into larger bundles. For the iodine exposed film, the fibrillar structure is present but small bundles with dimensions of several hundred Angstrom have formed throughout the network.