Cosmic rays may broadly be divided into two categories, primary and secondary. The cosmic rays that arise in extrasolar astrophysical sources are primary cosmic rays; these primary cosmic rays can interact with interstellar matter to create secondary cosmic rays. The sun also emits low energy cosmic rays associated with solar flares. The exact composition of primary cosmic rays, outside the Earth's atmosphere, is dependent on which part of the energy spectrum is observed. However, in general, almost 90% of all the incoming cosmic rays are protons, about 9% are helium nuclei (alpha particles) and nearly 1% are electrons. The ratio of hydrogen to helium nuclei (28% helium by mass) is about the same as the primordial elemental abundance ratio of these elements (24% by mass He) in the universe.

The remaining fraction is made up of the other heavier nuclei which are abundant end products of stars' nuclear synthesis. Secondary cosmic rays consist of the other nuclei which are not abundant nuclear synthesis end products, or products of the Big Bang, primarily lithium, beryllium, and boron. These light nuclei appear in cosmic rays in much greater abundance (about 1:100 particles) than in solar atmospheres, where their abundance is about 10−7 that of helium.

This abundance difference is a result of the way secondary cosmic rays are formed. When the heavy nuclei components of primary cosmic rays, namely the carbon and oxygen nuclei, collide with interstellar matter, they break up into lighter nuclei (in a process termed cosmic ray spallation) - lithium, beryllium and boron. It is found that the energy spectra of Li, Be and B fall off somewhat more steeply than those of carbon or oxygen, indicating that less cosmic ray spallation occurs for the higher energy nuclei presumably due to their escape from the galactic magnetic field. Spallation is also responsible for the abundances of scandium, titanium, vanadium, and manganese ions in cosmic rays, which are produced by collisions of iron and nickel nuclei with interstellar matter. (See environmental radioactivity#Natural).

In the past, it was believed that the cosmic ray flux has remained fairly constant over time. Recent research has, however, produced evidence for 1.5 to 2-fold millennium-timescale changes in the cosmic ray flux in the past forty thousand years.[3]