The best estimate simulation of three-dimensional phenomena in nuclear reactor cores requires the use of coupled neutron physics and thermal-hydraulics calculations. However these analyses should be supplemented by the survey of the corresponding uncertainties. In this paper the uncertainties of the coupled KIKO3D-ATHLET calculations are presented for a VVER-1000 type core using the OECD NEA Kalinin-3 (Phase II) benchmark data, although only the neutronic uncertainties are considered and further simplifications are applied and discussed. Additionally, this study has been performed in the conjunction with the OECD NEA UAM benchmark, as well. In the first part of the paper, the uncertainties of the effective multiplication factor, the assembly-wise radial power distribution, the axial power distribution, the rod worth, etc. are presented at steady-state. After that some uncertainties of the transient calculations are discussed for the considered switch-off of one Main Circulation Pump (MCP) type transient.