A novel preference chamber with four inter-connected compartments was designed and built to test the tolerance of atmospheric ammonia by laboratory mice. The preference chamber incorporated a novel tracking system using an infra-red sensor at each end of each tunnel, which monitored all journeys through the tunnels and their direction. An experiment was successfully undertaken with four batches, each of four mice. Each batch was housed in the chamber for 4 days and given the choice between ammonia concentrations of nominally 0, 25, 50 and 100 ppm after initial familiarization. The results showed that there were two motivations acting on mouse behavior. The mice made extensive use of the whole chamber once they had been trained to use the tunnels, at least 2000 movements between compartments for each group over 48 h. The mice clearly preferred to be in the upper two compartments of the top tier of the chamber rather than in the lower compartments. The mice did not exhibit a clear preference for or aversion to ammonia, which implies that their short- term tolerance of ammonia at potentially noxious concentrations may not be in their long-term interest.