It is well known that a fundamental theorem of Quantum Field Theory (QFT) set in flat spacetime ensures the CPT invariance of the theory. This symmetry is strictly connected to the Lorentz covariance, and consequently to the fundamental structure of spacetime. Therefore it may be interesting to investigate the possibility of departure from this fundamental symmetry, since it can furnish a window to observe possible effects of a more fundamental quantum gravity theory in a “lower energy limit”. Moreover, in the past, the inquiry of symmetry violations provided a starting point for new physics discoveries. A useful physical framework for this kind of search is provided by astroparticle physics, thanks to the high energy involved and to the long path travelled by particles accelerated by an astrophysical object and then revealed on Earth. Astrophysical messengers are therefore very important probes for investigating this sector, involving high energy photons, charged particles, and neutrinos of cosmic origin. In addition, one can also study artificial neutrino beams, investigated at accelerator experiments. Here we discuss the state of art for all these topics and some interesting new proposals, both from a theoretical and phenomenological point of view.