Most of the orbits of the Milky Way (MW) satellite galaxies and some of the orbits of the MW globular cluster system lie near Great Circles in the Sky. The existence of satellites in the same orbital plane could be understood if they were part of the same accretion event. However, this argument cannot explain, for example, the different star formation histories of dwarfs belonging to the same Great Circle. In this paper we will show, using hydrodynamical cosmological simulations, that the origin of Great Circles can be found in the filaments of cosmological structures, since satellites accreted along the same, or close, filaments will orbit the host roughly on the same plane.