Large scale noise exposure modelling is used in epidemiological research projects as well as for noise mapping and strategic action planning. Such calculations should always be accompanied by an assessment of uncertainty, on the one hand to check for systematic deviations and on the other hand to investigate the sources of uncertainty to address them in future studies. Within the SiRENE (Short and Long Term Effects of Transportation Noise Exposure) project, a large scale nationwide assessment of Switzerland’s road, railway, and aircraft noise exposure was conducted for the year 2011. In the present follow-up study, we equipped 180 sleeping and/or living room windows with sound level meters for one week. The resulting dataset was used to validate noise exposure modelling within SiRENE. For the noise metric LDEN the comparison revealed a difference of 1.6 ± 5 dB(A) when taking all measurements into account. After removing measurement sites with noise mitigation measures not considered in the modelling, the difference to the calculation was reduced to 0.5 ± 4 dB(A). As major sources of uncertainty, the position accuracy and topicality of infrastructure and building geometries, the traffic modelling as well as the acoustic source and propagation models were identified.