We have investigated the electrochemical synthetic mechanism of conductive polymer nanotubes in a porous alumina template using poly(3,4-ethylenedioxythiophene) (PEDOT) as a model compound. As a function of monomer concentration and potential, electropolymerization leads either to solid nanowires or to hollow nanotubes, and it is the purpose of these investigations to uncover the detailed mechanism underlying this morphological transition between nanowire and nanotube. Transmission electron microscopy was used to characterize electrochemically synthesized PEDOT nanostructures and measure the extent of their nanotubular portion quantitatively. The study on potential dependency of nanotubular portion shows that nanotubes are grown at a low oxidation potential (1.2 V vs Ag/AgCl) regardless of monomer concentration. This phenomenon is attributed to the predominance of electrochemically active sites on the annular-shape electrode at the pore bottom of a template. The explanation was supported by a further electrochemical study on a flat-top electrode. We elaborate the mechanism by taking into account the effect of electrolyte concentration, temperature, and template pore diameter on PEDOT nanostructures. This mechanism is further employed to control the nanotube dimensions of other conductive polymers such as polypyrrole and poly(3-hexylthiophene).