Abstract A regional assessment of the effective CO2 storage capacity within the Swedish Sector of the Baltic Sea Basin has been performed. Storage within several deep Cambrian sandstone aquifers, sealed by a thick sequence of Ordovician and Silurian limestone and marlstone, was investigated. Stratigraphic and structural traps were considered within the Faludden, När and Viklau aquifers. Effective CO2 storage capacities and associated uncertainty were calculated probabilistically, using methods outlined by the U.S. Department of Energy and the U.S. Geological Survey. Detailed characterisation of porosity, reservoir thickness, top reservoir structure, CO2 density and storage efficiency factor was performed. A Monte Carlo approach was adopted to generate distributions of effective storage capacity for the scenarios considered. Within the study area, the most suitable structural trap is the S41/Dalders structure, located in the southeastern part of the Swedish sector, with estimated low, mid and high storage capacities of 85Mt, 145Mt and 224Mt, respectively. The regional Faludden stratigraphic pinch out trap was assessed to have low, mid and high effective storage capacities of 4330Mt, 5579Mt and 6962Mt, respectively. The storage capacity methodology outlined here, that includes estimates of uncertainties, may be easily adapted to other areas of interests for geological storage of CO2.