Most of the volume of the Universe consists of the Intergalactic Medium (IGM), space between collapsed structures like galaxies and galaxy clusters. Extragalactic photons and charged particles that propagate through the Universe spend most of their time in the IGM and can be influenced by its properties. In this talk, I will present a few examples of how we can study fundamental physics from IGM-particles interaction. These include constraints on new light feebly interacting particles as dark photons and axions from resonant photon-new particle conversion, measurement of the intergalactic magnetic field and its influence on ultrahigh-energy cosmic rays and gamma-rays propagation.