The disutility of transfers in multimodal public transport goes beyond the additional walking and waiting times. Although the magnitude of this pure transfer penalty has been proven to be an essential element in the structural design of public transport lines, the scarce available research reveals a wide range of values. The aim of this paper is to develop and apply a framework to estimate the value perceived and assigned by commuters to this penalty. This framework includes all the other elements considered by users in the case of a trip involving (potential) transfers, in order to obtain the impact of each one. The framework is based on the discrete choices paradigm and applied to data collected in Madrid, Spain. The results show that the pure transfer penalty is comparable to a 15.2-17.7 equivalent increase in in-vehicle minutes; i.e. longer trips may be preferred to faster alternatives with transfers, even if the additional walking. and waiting times are zero. As well as the pure transfer penalty, the model also captures the effects of habit, crowding, walking, waiting and in-vehicle times, information, and the additional effect of intermodality on transfers.