Small pores in high specific surface clay-rich caprocks give rise to high capillary entry pressures and high viscous drag that hinder the migration of buoyant carbon dioxide CO2. We measured the breakthrough pressure and ensuing CO2 permeability through sediment plugs prepared with sand, silt, kaolinite and smectite, and monitored their volumetric deformation using high-pressure oedometer cells. The data show water expulsion and volumetric contraction prior to CO2 breakthrough, followed by preferential CO2 flow thereafter. Our experimental results and data gathered from previous studies highlight the inverse relationship between breakthrough pressure and pore size, as anticipated by Laplace’s equation. In terms of macro-scale parameters, the breakthrough pressure increases as the sediment specific surface increases and the porosity decreases. The breakthrough pressure is usually lower than the values predicted with average pore size estimations; it can reach ∼6.2MPa in argillaceous formations, and 11.2MPa in evaporites. The CO2 permeability after breakthrough is significantly lower than the absolute permeability, but it may increase in time due to water displacement and desiccation. Leakage will be advection-controlled once percolation takes place at most storage sites currently being considered. Diffusive and advective CO2 leaks through non-fractured caprocks will be minor and will not compromise the storage capacity at CO2 injection sites. The “sealing number” and the “stability number” combine the initial fluid pressure, the buoyant pressure caused by the CO2 plume, the capillary breakthrough pressure of the caprock, and the stress conditions at the reservoir depth; these two numbers provide a rapid assessment of potential storage sites. Unexpected CO2 migration patterns emerge due to the inherent spatial variability and structural discontinuities in geological formations; sites with redundant seal layers should be sought for the safe and long-term storage of CO2.