On January 16–22, 2005 huge fluxes of high-energy charged particles came from the Sun through magnetosphere to our Earth. Charged particles mostly solar protons and magnetospheric electrons affect the atmosphere by inducing additional ionization sources in ionosphere and atmosphere. Ionization plays main role in the formation of ozone-depleting odd oxides of nitrogen (NOx) and hydrogen (HOx). Here we study the energetic particle impact on the chemical properties of the stratosphere and mesosphere in the Northern Hemisphere using MLS Aura data obtained during January 16–22, 2005. We show how strong can be depleted the polar ozone layer in mesosphere and change the chemistry from the mesosphere to the stratosphere during geoeffective coronal mass ejections and magnetic storms.