Polyaniline (PAN) and polypyrrole (PPY) were analyzed by X-ray photoelectron spectroscopy (XPS) and bulk analytical techniques. A systematic comparison of the results was carried out to determine the effects of anion size, synthesis methods, and the nature of the polymer (powder or film) on the variation between the surface and bulk compositions. Good agreement between the XPS and bulk analytical results is generally obtained for chemically synthesized polyaniline (in powder form). However, these two methods may give substantial discrepancies in the analysis of anion concentration in as-cast polyaniline base films subjected to re-doping by acids. Such discrepancies are also found in the analysis of as-synthesized polypyrrole doped by large anions and polypyrrole base films and powders after re-doping by acids. In these cases the XPS technique tends to give anion concentrations that are significantly higher than the bulk values. In some of these cases the high surface anion concentration supports a high proportion of positively charged nitrogens (>50% for polyaniline, >30% for polypyrrole), which must involve the protonation of some amine units in addition to all of the imine units. However, in actuality, the re-doping process can only replenish the anions to less than half of the original bulk concentration in polypyrrole.