National and international carbon reporting systems require information on carbon stocks of forests. For this purpose, terrestrial assessment systems such as forest inventory data in combination with carbon estimation methods are often used. In this study we analyze and compare terrestrial carbon estimation methods from 12 European countries. The country-specific methods are applied to five European tree species (Fagus sylvatica L.;Quercus robur L.;Betula pendula Roth, Picea abies (L.) Karst.;Pinus sylvestris L.), using a standardized theoretically-generated tree dataset. We avoid any bias due to data collection and/or sample design by using this approach. We are then able to demonstrate the conceptual differences in the resulting carbon estimates with regard to the applied country-specific method. In our study we analyze (i) allometric biomass functions, (ii) biomass expansion factors in combination with volume functions and (iii) a combination of both. The results of the analysis show discrepancies in the resulting estimates for total tree carbon and for single tree compartments across the countries analyzed of up to 140. t. carbon/ha. After grouping the country-specific approaches by European Forest regions, the deviation within the results in each region is smaller but still remains. This indicates that part of the observed differences can be attributed to varying growing conditions and tree properties throughout Europe. However, the large remaining error is caused by differences in the conceptual approach, different tree allometry, the sample material used for developing the biomass estimation models and the definition of the tree compartments. These issues are currently not addressed and require consideration for reliable and consistent carbon estimates throughout Europe. © 2015 Elsevier B.V.