Abstract Non-energy use of fossil fuels accounts for 7% of the Total Primary Energy Supply (TPES) of Germany and represents an important potential source of CO 2 (carbon dioxide) emissions. To gain a better understanding of emissions associated with non-energy use in Germany, we conduct a bottom- up carbon flow analysis with the Non-energy use Emission Accounting Tables (NEAT) model for the period of 1990–2003. We calculate average yearly non-energy use emissions to be 25 ± 2 megatonnes (Mt) CO 2, of which 77% are related to industrial processes, 17% to solvent and other product use, 2% to fertilizer use in agriculture, and 4% to wastewater treatment. The comparison of NEAT estimates and official data reveals gaps and errors in the German greenhouse gas (GHG) inventory. This research highlights the difficulties associated with non-energy use emissions accounting not only in Germany but in other countries as well. To ensure correct calculation of non-energy use emissions, we recommend that inventory experts (i) obtain detailed insight into the system boundaries of non-energy use data as stated in national energy statistics, (ii) allocate non-energy use emissions accordingly to the relevant emission source categories (i.e., energy, industrial processes, solvent and other product use, agriculture, or waste), (iii) ensure completeness of emission estimates, and (iv) be cautious with the use of default emission factors as given by the Intergovernmental Panel on Climate Change (IPCC).