Carbon capture and storage (CCS) is seen as a key technology to tackle climate change. The principal idea of CCS is to remove carbon from the flue gases arising from burning fuels for electricity generation or industrial applications and to store the carbon in geological formations to prevent it from entering the atmosphere. Policy makers in several countries are supportive of the technology, but a number of uncertainties hamper its further development and deployment. The paper makes three related contributions to the literatures on socio-technical systems and technology assessment: 1) It systematically develops an interdisciplinary framework to assess the main uncertainties of CCS innovation. These include technical, economic, financial, political and societal issues. 2) It identifies important linkages between these uncertainties. 3) It develops qualitative and quantitative indicators for assessing these uncertainties. This framework aims to help decision making on CCS by private and public actors and is designed to be applicable to a wider range of low carbon technologies. The paper is based on a systematic review of the social science literature on CCS and on insights from innovation studies, as well as on interviews about assessment of new technologies with experts from a range of organisations and sectors.