Atmospheric neutrinos observed by IceCube detector, which are the main background in astrophysical neutrino searches, can be used to probe various beyond the standard model scenarios. I will discuss these probes, mostly the sterile neutrinos searches and non-standard neutrino interactions (NSI). Also, the sterile+NSI scenario, which recently has been proposed to relax the IceCube limits on sterile neutrinos, will be discussed. Other than these scenarios, I will discuss searches for large extra dimensions and violation of equivalence principle by atmospheric neutrinos.