We present a performance comparison of polythiophene/fullerene derivative bulk heterojunction solar cells fabricated on fluorinated tin oxide (FTO) and indium tin oxide (ITO) in the presence and absence of the commonly used poly(3,4-ethylenedioxythiophene): poly(styrenesulfonate) (PEDOT:PSS) hole extraction layer. From a potential commercial perspective the performance of cheaper and more readily available FTO compares well with the more expensive ITO in terms of measured device efficiency (FTO:2.8 % and ITO:3.1%). The devices show similar fill factors (FTO:63% and ITO:64%) with the same open circuit voltage of 0.6 V. The short circuit current density is lower for FTO devices at 7.5 mA/cm2 which compares with 8.0 mA/cm2 for ITO; a behaviour that is mainly attributed to the reduced optical transmission of the FTO layer. Importantly, these devices were part fabricated and wholly characterized under atmospheric conditions. The quoted device performance is the best reported for FTO based bulk heterojunction systems in the absence of the highly acidic PEDOT:PSS hole extraction layer, which is believed to degrade conductive oxides.