A brief review of the study during COST Action ES0803 of effects due to cosmic rays (CR) and solar energetic particles (SEP) in the ionosphere and atmosphere is presented. Models CORIMIA (COsmic Ray Ionization Model for Ionosphere and Atmosphere) and application of CORSIKA (COsmic Ray SImulations for KAscade) code are considered. They are capable to compute the cosmic ray ionization profiles at a given location, time, solar and geomagnetic activity. Intercomparison of the models, as well as comparison with direct measurements of the atmospheric ionization, validates their applicability for the entire atmosphere and for the different levels of the solar activity. The effects of CR and SEP can be very strong locally in the polar cap regions, affecting the physical-chemical and electrical properties of the ionosphere and atmosphere. Contributions here were also made by the anomalous CR, whose ionization is significant at high geomagnetic latitudes (above 65°-70°). Several recent achievements and application of CR ionization models are briefly presented. This work is the output from the SG 1.1 of the COST ES0803 action (2008)(2009)(2010)(2011)(2012) and the emphasis is given on the progress achieved by European scientists involved in this collaboration.