The primary trapping mechanism in CO2 storage is structural trapping, which means accumulation of a CO2 column under a deformation in the caprock. We present a study on how different top-seal morphologies will influence the CO2 storage capacity and migration patterns. Alternative top-surface morphologies are created stochastically by combining different stratigraphic scenarios with different structural scenarios. Stratigraphic surfaces are generated by Gaussian random fields, while faults are generated by marked point processes. The storage capacity is calculated by a simple and fast spill-point analysis, and by a more extensive method including fluid flow simulation in which parameters such as pressure and injection rate are taken into account. Results from the two approaches are compared. Moreover, by generating multiple realizations, we quantify how uncertainty in the top-surface morphology impacts the primary storage capacity. The study shows that the morphology of the top seal is of great importance both for the primary storage capacity and for migration patterns.