The large solar storms in October--November 2003 produced enormous solar proton events (SPEs) where high energetic particles reached the Earth and penetrated into the middle atmosphere in the polar regions. At this time, the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) was observing the atmosphere in the 6--68 km altitude range. MIPAS observations of NOx (NO + NO2) and O3 of the period from 25 October to 14 November 2003 are the first global measurements of NOx species, covering both the summer (daylight) and winter (dark) polar regions during an SPE. Very large values of NOx in the upper stratosphere of 180 ppbv (parts per billion by volume) have been measured, and a large asymmetry in northern and southern polar cap NOx enhancements was found. Arctic mean polar cap (>60¿) NOx enhancements of 20 to 70 ppbv between 40 to 60 km lasted for at least 2 weeks, while the Antarctic mean NOx enhancement was between 10 and 35 ppbv and was halved after 2 weeks. Ozone shows depletion signatures associated with both HOx (H + OH + HO2) and NOx enhancements but at different timescales. Arctic lower mesospheric (upper stratospheric) ozone is reduced by 50--70% (30--40%) for about 2 weeks after the SPEs. A smaller ozone depletion signal was observed in the Antarctic atmosphere. After the locally produced Arctic middle and upper stratospheric as well as mesospheric NOx enhancement, large amounts of NOx were observed until the end of December. These are explained by downward transport processes. These enhancements drastically declined with the mid-December stratospheric warming. Significant O3 depletion was observed inside the polar vortex in a wide altitude range during this period. From mid-January until the end of March 2004, MIPAS observed extraordinary high values of NO2 in the upper stratosphere of the northern polar region (mean in-vortex values up to 350 ppbv at ~54 km), which seem to be caused by the unusually strong vortex and downward transport at that time together with an uncommonly large auroral activity starting with the solar storms in October--November and continuing over the winter. In-vortex ozone was observed to significantly decline in the mid-February to late March period above the 1750 K potential temperature level.