Background Denmark has implemented a comprehensive, nationwide pharmaceutical information system, and this system has been evaluated by the Danish Council of Ethics. The system can be seen as an exemplar of a comprehensive health information system for clinical use. Analysis The paper analyses 1) how informed consent can be implemented in the system and how different implementations create different impacts on autonomy and control of information, and 2) arguments directed towards justifying not seeking informed consent in this context. Results and (...) Conclusion Based on the analysis a heuristic is provided which enables a ranking and estimation of the impact on autonomy and control of information of different options for consent to entry of data into the system and use of data from the system. The danger of routinisation of consent is identified. The Danish pharmaceutical information system raises issues in relation to autonomy and control of information, issues that will also occur in relation to other similar comprehensive health information systems. Some of these issues are well understood and their impact can be judged using the heuristic which is provided. More research is, however needed in relation to routinisation of consent. (shrink)