Strategic environmental assessment (SEA) is a widely applied policy tool that aims to aid decision-makers in making informed, higher-quality decisions that minimize negative environmental impacts. However, different types of uncertainties complicate the ex ante assessment of environmental impacts. Literature suggests uncertainties are often not well addressed, resulting in inaccurate and even unreliable SEAs. At the same time, SEA literature offers limited guidance in how to systematically identify and deal with uncertainties. Therefore, in this paper, we present an analytical framework for characterizing and classifying different forms of uncertainty in SEA, and for identifying strategies for dealing with these uncertainties. The framework is based on literature on uncertainties in other subdomains of the environmental sciences. The framework is applied to five case studies of SEAs for spatial planning in The Netherlands in order to illustrate and critically reflect on our framework, and to bridge the gap between theory and practice. Based on these case studies we concluded the following: (1) The framework is useful for identifying uncertainties in SEA in a systematic way; (2) There is a discrepancy between how uncertainties are dealt with in theory and in practice; (3) In practice, uncertainties seem to be dealt with in a rather implicit way. The framework may help dealing with uncertainties more systematically and more proactively; (4) The most successful way of coping with uncertainties seems to be the application of multiple strategies.