Existing methods for analysis of home cage-based preference tests are either time-consuming, not suitable for group management, expensive, and/or based on proprietary equipment that is not freely available. To correct this, we developed an automated system for group-housed mice based on radio frequency identification: the Mouse Position Surveillance System (MoPSS). The system uses an Arduino microcontroller with compatible components; it is affordable and easy to rebuild for every laboratory because it uses free and open-source software and open-source hardware with the RFID readers as the only proprietary component. The MoPSS was validated using female C57BL/6J mice and manual video comparison. It proved to be accurate even for fast-moving mice (up to 100% accuracy after logical reconstruction), and is already implemented in several studies in our laboratory. Here, we provide the complete construction description as well as the validation data and the results of an example experiment. This tracking system will allow group-based preference testing with individually identified mice to be carried out in a convenient manner. This facilitation of preference tests creates the foundation for better housing conditions from the animals’ perspective.