In this manuscript, we describe a biocompatible organic electrode system, comprising poly(3,4-ethylenedioxythiophene) (PEDOT) microelectrode arrays on indium tin oxide (ITO) glass, that can be used to regulate the neuron type, location, polarity, and outgrown length of neuron-like cells (PC-12). We fabricated a PEDOT microelectrode array with four different sizes (flat; 20, 50, and 100 μm) through electrochemical polymerization. Extracellular matrix proteins absorbed well on these organic electrodes; cells absorbed selectively on the organic electrodes when we used polyethylene oxide/polypropylene oxide/polyethylene oxide triblock copolymers (PEO/PPO/PEO, Pluronic™ F108) as the anti-adhesive coating. In this system, the neurite polarities and neuron types could be manipulated by varying the width of the PEDOT microelectrode arrays. On the unpatterned PEDOT electrode, PC-12 cells were randomly polarized, with approximately 80% having multi-polar cell types. In contrast, when we cultured PC-12 cells on the 20 μm wide PEDOT line array, the neurites aligned along the direction of the organic electrodes, with the percentage of uni- and bipolar PC-12 cells increasing to greater than 90%. The outgrowth of neurites on the microelectrodes was promoted by ∼60% with an applied electrical stimulation. Therefore, these electroactive PEDOT microelectrode arrays have potential for use in tissue engineering related to the development and regeneration of mammalian nervous systems.