The Whole Atmosphere Community Climate Model (WACCM3) has been used to study the long-term (more than a few months) effects of solar proton events (SPEs). Extremely large solar proton events occurred in 1972, 1989, 2000, 2001, and 2003 and caused some longer-lasting atmospheric changes. The highly energetic solar protons produced odd hydrogen (HOx) and odd nitrogen (NOy), which then led to ozone variations. Some statistically significant long-term effects on mesospheric ozone were caused by the HOx increases due to a very active time period for SPEs (years 2000–2004), even though the HOx increases were short-lived (days). The long-term stratospheric ozone effects were caused by the NOy enhancements. Very large NOy enhancements lasted for months in the middle and lower stratosphere after a few of the largest SPEs. SPE-caused NOy increases computed with WACCM3 were statistically significant at the 95% level throughout much of the polar stratosphere and mesosphere in the recent solar maximum 5-year period (2000–2004). WACCM3-computed SPE-caused polar stratospheric ozone decreases of >10% continued for up to 5 months past the largest events; however, statistically significant ozone decreases were computed for only a relatively small fraction of this time in relatively limited altitudes in the lower mesosphere and upper stratosphere. Annually averaged model output showed statistically significant (to 95%) stratospheric ozone loss in the polar Northern Hemisphere for years 2000–2002. The computed annually averaged temperature and total ozone change in these years were not statistically significant.