Design floods for a given location at a stream can be estimated by a number of approaches including flood frequency statistics and the design storm method. If applied to the same catchment the two methods often yield quite different results. The aim of this paper is to contribute to understanding the reasons for these differences. A case study is performed for 10 alpine catchments in Tyrol, Austria, where the 100-year floods are estimated by (a) flood frequency statistics and (b) an event based runoff model. To identify the sources of the differences of the two methods, the 100-year floods are also estimated by (c) Monte Carlo simulations using a continuous runoff model. The results show that, in most catchments, the event based model gives larger flood estimates than flood frequency statistics. The reasons for the differences depend on the catchment characteristics and different rainfall inputs that were applied. For catchments with a high storage capacity the Monte Carlo simulations indicate a step change in the flood frequency curve when a storage threshold is exceeded which is not captured by flood frequency statistics. Flood frequency statistics therefore tends to underestimate the floods in these catchments. For catchments with a low storage capacity or significant surface runoff, no step change occurs, but in three catchments the design storms used were larger than those read from the IDF (intensity duration frequency) curve leading to an overestimation of the design floods. Finally, also the correct representation of flood dominating runoff components was shown to influence design flood results. Geologic information on the catchments was essential for identifying the reasons for the mismatch of the flood estimates.