Electrodes intended for neural communication must be designed to meet both the electrochemical and biological requirements essential for long term functionality. Metallic electrode materials have been found inadequate to meet these requirements and therefore conducting polymers for neural electrodes have emerged as a field of interest. One clear advantage with polymer electrodes is the possibility to tailor the material to have optimal biomechanical and chemical properties for certain applications. To identify and evaluate new materials for neural communication electrodes, three charged biomolecules, fibrinogen, hyaluronic acid (HA), and heparin are used as counterions in the electrochemical polymerization of poly(3,4-ethylenedioxythiophene) (PEDOT). The resulting material is evaluated electrochemically and the amount of exposed biomolecule on the surface is quantified. PEDOT:biomolecule surfaces are also studied with static contact angle measurements as well as scanning electron microscopy and compared to surfaces of PEDOT electrochemically deposited with surfactant counterion polystyrene sulphonate (PSS). Electrochemical measurements show that PEDOT:heparin and PEDOT:HA, both have the electrochemical properties required for neural electrodes, and PEDOT:heparin also compares well to PEDOT:PSS. PEDOT:fibrinogen is found less suitable as neural electrode material.