In the present paper, the application of the in situ Fourier transform infrared (FTIR) attenuated total reflection (ATR) spectroscopy for the study of structural and electronic changes during electrochemically induced insulator-to-metal transitions of polyaniline (PANI) in aqueous electrolytes is reported. Problems concerning the discrimination of polymer absorption bands and anion absorption bands are discussed and perrhenate as a new doping system is presented. The infrared absorption bands of perrhenate do not interfere with the absorption bands of PANI and can therefore be used to determine in situ the changes of the anion content during electrochemical reactions of the polymer by an infrared spectroscopic method. The results of in situ FTIR ATR spectroscopy using a metal grid coated reflection element show that the method can yield important information for the elucidation of the reaction mechanisms of conductive polymers.