Abstract. Both aleatory and epistemic uncertainties associated with different sources and components of risk (hazard, exposure, vulnerability) are present at each step of seismic risk assessments. All individual sources of uncertainty contribute to the total uncertainty, which might be very high and, within the decision-making context, may therefore lead to either very conservative and expensive decisions or the perception of considerable risk. When anatomizing the structure of the total uncertainty, it is therefore important to propagate the different individual uncertainties through the computational chain and to quantify their contribution to the total value of risk. The present study analyses different uncertainties associated with the hazard, vulnerability and loss components by the use of logic trees. The emphasis is on the analysis of epistemic uncertainties, which represent the reducible part of the total uncertainty, including a sensitivity analysis of the resulting seismic risk assessments with regard to the different uncertainty sources. This investigation, being a part of the EU FP7 project MATRIX (New Multi-Hazard and Multi-Risk Assessment Methods for Europe), is carried out for the example of, and with reference to, the conditions of the city of Cologne, Germany, which is one of the MATRIX test cases. At the same time, this particular study does not aim to revise nor to refine the hazard and risk level for Cologne; it is rather to show how large are the existing uncertainties and how they can influence seismic risk estimates, especially in less well-studied areas, if hazard and risk models adapted from other regions are used.