In the last few years, use of thorium in fast reactors has been gaining increasing attention due to its favorable features in terms of waste minimization and resource availability. In particular, use of thorium in a closed cycle leads to a limited build-up of transuranic isotopes, and to a lower radio-toxicity generation. Unfortunately, U233 breeding is always accompanied by the production of undesirable U232, which represents a serious radiological hazard to workers during fuel reprocessing and, in particular, fabrication. A possible way to partially overcome such difficulty would be to avoid fuel pin fabrication through the development of liquid-fuelled reactors, among which the most promising ones are the Molten Salt Reactors. The present paper investigates the fuel cycle performances of the reference GEN-IV Molten Salt Fast Reactor (MSFR) in terms of isotope evolution, radio-toxicity generation and safety parameters, considering different fuel cycle strategies. Main results are also compared with those obtained for the GEN-IV ELSY Lead Fast Reactor. Calculations are performed by means of the EQL3D procedure developed at the Paul Scherrer Institut (Switzerland) for the analysis of equilibrium fuel cycles in fast reactors. In order to take into account the peculiarities of the MSFR design, a modified version of the procedure is proposed and adopted to model on-line reprocessing and the presence of blankets.