The need to reduce carbon emissions, via exploring the CO2 storage potential in the depleted subsurface hydrocarbon and the deep saline aquifers in the Baltic Basin region of Lithuania, is discussed. The paper presents a unique methodology, using multi-deterministic numerical models, for evaluating the CO2 storage potential of the deep saline aquifers and the depleted hydrocarbon fields of Lithuania. Such an approach has never been presented before for evaluation of Lithuanian subsurface reservoirs for CO2 storage potential. The paper also explains the limitations of previous estimates of CO2 storage potential computed for deep saline aquifers in Lithuania and introduces a new study that uses uncertainty quantification principle and numerical modelling to estimate the maximum CO2 injection and storage potential in the region. Three deep saline aquifers D11 (offshore), Syderiai and Vaskai (on shore) are evaluated along with depleted hydrocarbon reservoirs of Gargzdai residual oil zone. Evaluation estimates presented in this paper suggest a maximum theoretical storage potential in range of 96 –407 Mt. of CO2 for the three deep saline aquifers and in range of 64–267 Mt. of CO2 for Gargzdai residual oil zone. Although the primary focus of this paper is on the storage capacity estimation, a high-level analysis of the risks associated with CO2 injection and storage are also presented.