The ionosphere is an ionized layer extending from about 50 km to 1,000 km of altitude. When an electromagnetic signal cross this layer it suffers a delay in its group velocity and an advance in its phase velocity. The ionosphere is very dynamics and after the sunset its F region equatorial bottomside is lifted up by the intensified eastward electric field, giving origin to an steep plasma gradient. This configurates an unstable condition with higher density plasma standing over lower density one. This instability pushes rarified plasma upward giving origin to large regions named Equatorial Plasma Bubbles (EPB) that rise at equatorial regions and map to low latitudes along the magnetic field lines and can reach continental extension. Through cascating process small scale irregularities (cm to km) are generated inside the EPBs. Due to refractive effects amplitude and phase scintillations are generated in the signal crossing these irregularities. Trans-ionospheric signals used in telecommunication links and in the GNSS applications are severely affected during ionospheric scintillations. In this work we will present the ionospheric scintillation morphology over Brazilian longitudinal sector, its effects over positioning and navigation systems and the existing methodology to mitigate them.