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Strategies for mitigating global climate change require accurate estimates of the emissions of greenhouse gases (GHGs). A strong consensus in the global scientific community states that efforts to control climate change require stabilization of the atmospheric concentration of GHGs (as per a recent compilation; (IPCC 2013)). Estimates of the amounts of carbon dioxide and other GHGs emitted to the atmosphere, as well as the amounts absorbed by terrestrial and aquatic systems, are crucial for planning, analyzing, validating and at global scale verifying mitigation efforts and for analyzing scenarios of future emissions. The magnitude and distribution of current emissions and the path of future emissions are both of considerable importance. It is critical that we have estimates of emissions and that we acknowledge and deal with the uncertainty in our best estimates. The range of issues that derive from uncertainty in emissions estimates was the subject of the 3rd International Uncertainty Workshop held in Lviv, Ukraine, 2010, and is the subject of this special issue.