This paper develops a methodology for testing and implementing differences in preferences for a set of public transport modes, relating to observed and unobserved attributes, in state-of-practice large-scale travel demand models. Results of a case study for commuters in the Stockholm public transport system suggest that there are preference differences among public transport modes, and that they are captured by unobserved attributes. Surprisingly, we found no evidence for differences proportional to the in-vehicle time, suggesting that characteristics of in-vehicle time in different public transport modes, such as comfort, are valued equally by the travellers. We also found that the value of time is higher for auxiliary modes than for the main mode, and that the unobserved preference for metro is highest and the preference for light rail lowest.