In the present paper an uncertainty analysis on an application of the commercial urban drainage model MOUSE is conducted. Applying the Generalized Likelihood Uncertainty Estimation (GLUE) methodology the model is conditioned on observation time series from two flow gauges as well as the occurrence of combined sewer overflow. The GLUE methodology is used to test different conceptual setups in order to determine if one model setup gives a better goodness of fit conditional on the observations than the other. Moreover, different methodological investigations of GLUE are conducted in order to test if the uncertainty analysis is unambiguous. It is shown that the GLUE methodology is very applicable in uncertainty analysis of this application of an urban drainage model, although it was shown to be quite difficult to get good fits of the whole time series.