During a polarity transition of the Earth's magnetic field, the structure and strength of the field change significantly from their present values. This will alter the global pattern of charged particle precipitation into the atmosphere. Thus, particle precipitation is possible into regions that are at the moment effectively shielded by the Earth's magnetic field. A two-dimensional global chemistry, photolysis and transport model of the atmosphere has been used to investigate how the increased particle precipitation affects the chemical composition of the middle and lower atmosphere. Ozone losses resulting from large energetic particle events are found to increase significantly, with resultant losses similar to those observed in the Antarctic ozone hole of the 1990s. This results in significant increases in surface UV-B radiation as well as changes in stratospheric temperature and circulation over a period of several months after large particle events.