Abstract: A variety of sources, including gamma-ray bursts, supernovae, X-ray flashes, solar flares, and a galactic bow/termination shock may intermittently produce photon and/or cosmic ray proton fluxes of sufficient intensity to damage the atmosphere of a terrestrial type planet. A typical interval for major irradiations, which are candidates for extinction events, may be of order 100 My for the Earth. The dominant effect is ionization and dissociation of molecules in the atmosphere, which leads to the formation of ozone-depleting compounds. This in turn allows greatly increased penetration of UVB from the Sun, resulting in DNA and protein damage, including major effects on phytoplankton. Other effects should include (1) direct irradiation of organisms from cosmic-ray secondaries with similar results, and (2) the nucleation of water droplets resulting in increased low-level cloud cover, which may induce climate cooling due to albedo increases. Other possible effects include visible light opacity from NO2, enhanced nitrate deposition from atmospheric chemistry changes, and endocrine effects from blue light. Mars and Europa type planets have obviously very different vulnerabilities. Numerical modeling has led to some simplifying principles which allow back-of-the-envelope estimation of ionizing photon effects on the Earth.