To unify the standard model of particle physics and general relativity, we may require a quantum description of gravity, which will change our notion of spacetime at very high energies. In this dissertation we explore possible traces of new physics beyond special relativity, using the propagation of high energy astroparticles. For this purpose, the two ways of going beyond Lorentz invariance are presented, a breaking of the Lorentz invariance (Lorentz invariance violation or LIV or its deformation (doubly special relativity or DSR), emphasizing their conceptual and phenomenological differences. For the study of LIV, the work focuses on the prediction of modifications in the expected neutrino flux on Earth, both from astrophysical and cosmogenic origin (from the interaction of cosmic rays with the background radiation during their propagation). For the study of DSR we focus instead on the search for anomalies in the time of flight of massless particles (time delays) and on the study of the expected flux of gamma rays on Earth. The results obtained show the possibility of using astroparticle observations as a window to quantum gravity phenomenology, at energies attainable at present and/or in the very near future.