In this study, we prepared a poly(3,4-ethylenedioxythiophene) (PEDOT) modified electrode by the electropolymerization of 0.01 M 3,4-ethylenedioxythiophene at a screen-printed electrode (SPE) in the presence of 0.1 M LiClO4 and 5 mM hydroxypropyl-β-cyclodexdrine. Many bio-interests were selected as test analytes. Electrochemical oxidation of cysteine in various pH buffer solutions (pH 2.0 ~12.0) was conducted at the SPE/PEDOT modified electrodes. Cyclic voltammetric studies showed that the SPE/PEDOT modified electrodes possessed great catalytic activity toward cysteine oxidation, and the best catalytic responses occurred in pH 6.0 buffer solution. Flow injection analysis (FIA) coupled amperometric detection was used in order to decrease detection limit. The FIA conditions were examined and the FIA signals were optimized. A linear calibration plot was obtained for 0.05-200 μM cysteine with a slope of 0.0527 μA/μM. The detection limit (S/N = 3) was 0.03 μM. The relative standard deviation was 1.44, 1.77, 2.88% for 3 continuous injection of 0.5, 20, 200 μM cysteine standards, respectively. Determination of cysteine in real sample was conducted using the same approach. We prepared three real samples, root beer syrup, human urine, and aspirin, as back ground solutions. The recovery of cysteine from real sample was determined using the standard addition method and the mean recovery was 93.5% and 105.0% for root beer syrup and aspirin, respectively. In the human urine real sample, the cysteine oxidation current were decreased. Moreover, we discovered that the PEDOT thin film may adsorb benzoquinone (BQ) and catechol (CA) in solution. The prepared SPE/PEDOT/BQ and SPE/PEDOT/CA modified electrodes can used for electrochemical detections of AA and NADH.