To further improve the efficiency of the wafer-based silicon photovoltaic (PV) module, producers are introducing new module designs with cut-cells. Since smaller solar cells might be affected by partial shading even more and earlier than full-size cells, the energy performance simulations of partially shaded modules are crucial. A detailed shading analyses of partially shaded modules with different cut cell designs are presented not only on a single case scenario but on annual energy yield simulations using Spice, where a shading scenario over the whole module by the use of a new 3D shading horizon profile of selected shading objects is calculated. The annual simulations reveal that regardless the module design almost all cells in the module are confronted by reverse bias, which can deteriorate the module performance significantly. Simulation results with three different shading objects on five different module topologies at five locations showed that the best cut-cell module design depends strongly by the micro location and shading objects; however, in general the string of solar cells connected in series should be aligned with the shading shape around noontime as much as possible. A comprehensive annual energy performance evaluation of partially shaded cut-cell modules revealed; that with a correct cell layout of cut-cells in a PV module, the shading losses can be reduced by 30-50% if comparing to the standard PV module design. (c) 2020 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).