This study presents experiments designed to study the stability of the conducting polymer poly(3,4‐ethylene dioxythiophene) (PEDOT), under simulated physiological conditions using phosphate‐buffered saline (PBS) and hydrogen peroxide (H2O2) (0.01M) at 37°C over a 5‐ to 6‐week period. Voltage pulsing in PBS was used as an additional test environment. The influence of switching the counter ion used in electropolymerization from polystyrene sulphonate (PSS) to heparin was investigated. Absorbance spectroscopy and cyclic voltammetry were used to evaluate the material properties. Most of the samples in H2O2 lost both electroactivity and optical absorbance within the study period, but PEDOT:PSS was found slightly more stable than PEDOT:heparin. Polymers were relatively stable in PBS throughout the study period, with around 80% of electroactivity remaining after 5 weeks, disregarding delamination, which was a significant problem especially for polymer on indium tin oxide substrates. Voltage pulsing in PBS did not increase degradation. The counter ion influenced the time course of degradation in oxidizing agents. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 2010