Use of thorium in fast reactors has typically been considered as a secondary option, mainly thanks to a possible self-sustaining thorium cycle already in thermal reactors and due to the limited breeding capabilities compared to U–Pu in the fast neutron energy range. In recent years nuclear waste management has become more important, and the thorium option has been reconsidered for the claimed potential to burn transuranic waste and the lower build-up of hazardous isotopes in a closed cycle. To ascertain these claims and their limitations, the fuel cycle isotopic inventory, and associated waste radio-toxicity and decay heat, should be quantified and compared to the case of the uranium cycle using realistic core configurations, with complete recycle of all the actinides. Since the transition from uranium to thorium fuel cycles will likely involve a transuranic burning phase, this transition and the challenges that the evolving fuel actinide composition presents, for instance on reactor feedback parameters, should also be analyzed. In the present paper, these issues are investigated based on core physics analysis of the Lead-cooled Fast Reactor ELSY, performed with the fast reactor ERANOS code and the EQL3D procedure allowing full-core characterization of the equilibrium cycle and the transition cycles. In order to compute radio-toxicity and decay heat, EQL3D has been extended by developing a new module, which has been assessed against ORIGEN-S and is presented here. The capability of the EQL3D procedure to treat full-core 3D geometries allowed to explicitly account for aspects related to core dimensions and safety parameters in the analysis, giving a better insight into the pros and cons of the thorium option.