In this paper, the parameters in a building thermal simulation model are tracked, which are subject to modeling uncertainty, i.e. uncertainty arising from commonly applied physical assumptions and simplifications. As an example, the simulation of the thermal comfort performance of a naturally ventilated office building without cooling plant is analyzed. The sensitivity of the simulated performance to the uncertainty in the parameters is investigated with a factorial sampling technique, which not only estimates the mean parameter effects, but also reveals the relative importance of non-linear effects and parameter interactions.