Electrochemical deposition of the conjugated polymer poly(3,4-ethylenedioxythiophene) (PEDOT) forms thin, conductive films that are especially suitable for charge transfer at the tissue-electrode interface of neural implants. For this study, the effects of counter-ion choice and annealing parameters on the electrical and structural properties of PEDOT were investigated. Films were polymerized with various organic and inorganic counter-ions. Studies of crystalline order were conducted via X-ray diffraction (XRD). Electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV) were used to investigate the electrical properties of these films. X-ray photoelectron spectroscopy (XPS) was used to investigate surface chemistry of PEDOT films. The results of XRD experiments showed that films polymerized with certain small counter-ions have a regular structure with strong (100) edge-to-edge correlations of PEDOT chains at ~1.3 nm. After annealing at 170 °C for 1 hour, the XRD peaks attributed to PEDOT disappeared. PEDOT polymerized with LiClO(4) as a counter-ion showed improved impedance and charge storage capacity after annealing at 160 °C.