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Changes in soil organic carbon (SOC) stocks in Switzerland’s mineral agricultural soils are simulated using RothC, the results of which are used for national GHG reporting. A sensitivity analysis of these simulations and of the system used to upscale these simulations to the national scale is described in this report. The main aim of the analysis was to understand which input or model parameters need to be estimated more precisely or accurately in the future and thus where resources need to be prioritised. A Monte Carlo approach was used, varying all parameters simultaneously. The input and model parameters were set to vary i. by a fixed amount and ii. according to their uncertainty or the variation they are expected to vary by in reality. The latter allowed the importance of parameters to be judged, as both model sensitivity and extent of variation of the parameters are considered. The change in SOC stocks over 28 years was used as the response variable. Changes in SOC stocks in cropland, in year-round managed grassland and in summer pasture areas were investigated separately. Although the results for these three land use types differ, a common set of parameters important for all of them was identified (the carbon use efficiency scaling factor, the decay rate constants of the humified organic matter and resistant plant matter C pools, initial SOC, temperature and precipitation). The variation of the two latter parameters is mainly due to the sometimes large regions that are used for the upscaling of simulations to the national scale, rather than uncertainty in the parameter estimates themselves. A move to simulating smaller regions, for example raster-based modelling, would therefore improve the simulation of SOC changes greatly. The estimate of the former three parameters (all model parameters) will on the other hand not be improved with simulations at higher spatial resolution and should be prioritised for future research. Lastly, we show that a model parameter associated with topsoil moisture deficit becomes more important in years with hot and dry summers; this parameter is likely to be very important for countries with frequent drought and will become more important for Switzerland in the future. Though the analysis pertains to the Swiss inventory system, it aims to provide information that can be used in other countries or regions, or for the improvement of the RothC model in general.