In this chapter, the authors summarize their understanding of Poly(3,4-ethylenedioxythiophene) (PEDOT), with respect to its chemical and physical fundamentals. They focus upon the structure of several PEDOT systems, from the angstrom level and up, and the impact on both electronic and ionic transport. The authors discuss the structural properties of PEDOT:X and PEDOT:poly(styrenesulfonate) based on experimental data probed at the scale ranging from angstrom to submicrometer. The morphology of PEDOT is influenced by the nature of counter-ions, especially at high oxidation levels. The doping anions intercalate between PEDOT chains to form a “sandwich” structure to screen the positive charges in PEDOT chains. The authors provide the main transport coefficients such as electrical conductivity s, Seebeck coefficient S, and Peltier coefficient σ, starting from a general thermodynamic consideration. The optical conductivity of PEDOT has also been examined based on the effective medium approximation, which is normally used to describe microscopic permittivity properties of composites made from several different constituents.