The mechanisms of the influence of various energetic particles on the atmosphere and their consideration by modern models are discussed. The types of energetic particles considered are galactic cosmic rays, auroral electrons, solar protons, and electrons precipitating into the atmosphere from outer radiation belt. The effects of these particles on the ozone layer and climate are illustrated using observational data and model calculations. The influence of galactic cosmic rays is noticeable only in the troposphere at southern latitudes, whereas a strong but short-term destruction of ozone by episodic solar protons have no effect at climatic time scales. Thus, the main influence on the long-term ozone layer variability is exerted by energetic electrons. Changing ozone contents lead to changing heating rates, temperature, and structure of stratospheric circulation, which in turn affects wave processes and climate. Simulation of these processes requires the use of complex numerical models that include all necessary processes and their interaction in the atmosphere from the surface to the upper thermosphere.