Quantifying greenhouse gas emissions Abstract The assessment of greenhouse gases (GHGs) and air pollutants emitted to and removed from the atmosphere ranks high on international political and scientific agendas. Growing international concern and cooperation regarding the climate change problem have increased the need to consider the uncertainty in inventories of GHG emissions. The approaches to address uncertainty discussed in this special issue reflect attempts to improve national inventories, not only for their own sake but also from a wider, system analytic perspective. They seek to strengthen the usefulness of national emission inventories under a compliance and/or global monitoring and reporting framework. The papers in this special issue demonstrate the benefits of including inventory uncertainty in policy analyses. The issues raised by the authors and featured in their papers, along with the role that uncertainty analysis plays in many of their arguments, highlight the challenges and the importance of dealing with uncertainty. While the Intergovernmental Panel on Climate Change (IPCC) clearly stresses the value of conducting uncertainty analyses and offers guidance on executing them, the arguments made here in favor of performing these studies go well beyond any suggestions made by the IPCC to date. Improving and conducting uncertainty analyses are needed to develop a clear understanding and informed policy. Uncertainty matters and is key to many issues related to inventorying and reducing emissions. Considering uncertainty helps to avoid situations that can create a false sense of certainty or lead to invalid views of subsystems. Dealing proactively with uncertainty allows for the generation of useful knowledge that the international community should have to hand while strengthening the 2015 Paris Agreement, which had been agreed at the 21st Conference of the Parties to the United Nations Framework Convention on Climate Change (UNFCCC). However, considering uncertainty does not come free. Proper treatment of uncertainty is demanding because it forces us to take the step from “simple to complex” and to grasp a holistic system view. Only, thereafter, can we consider potential simplifications. That is, comprehensive treatment of uncertainty does not necessarily offer quick or easy solutions for policymakers. This special issue brings together 13 papers that resulted from the 2015 (4th) International Workshop on Uncertainty in Atmospheric Emissions, in Cracow, Poland. While they deal with many different aspects of the uncertainty in emission estimates, they are guided by the same principal question: “What GHGs shall be verified at what spatio-temporal scale to support conducive legislation at local and national scales, while ensuring effective governance at the global scale?” This question is at the heart of mitigation and adaptation. It requires an understanding of the entire system of GHG sources and sinks, their spatial characteristics and the temporal scales at which they react and interact, the uncertainty (accuracy and/or precision) with which fluxes can be measured, and last but not least, the consequences that follow from all of the aforementioned aspects, for policy actors to frame compliance and/or global monitoring and reporting agreements. This bigger system context serves as a reference for the papers in the special issue, irrespective of their spatio-temporal focus, and is used as a guide for the reader.