Pressure fluctuations caused by instabilities in the boundary layer are among the causes which lead to transition on a space vehicle during atmospheric re-entry. The knowledge of these unsteady fluctuations could help to identify the mechanisms which take part into the transition process and better predict them. In this framework and in support of the EXPERT PL4/PL5 post-flight analysis, surface pressure measurements have been performed in the VKI H3 Hypersonic Wind Tunnel. A 7deg half-angle cone with exchangeable nosetip was equipped with a stream-wise array of high frequency pressure transducers (PCB 132A31). Instabilities in the boundary layer have been investigated on a smooth surface and behind an isolated roughness element. Experimental data are then compared with linear stability theory computations, in support to the e^N transition prediction method and to the calibration of the ground facility. The results provided on a simplified ground test model, show the growth of second mode waves under a laminar boundary layer and their break down to turbulence as a function of Reynolds number and streamwise location. Moreover the effect of an isolated roughness element on the boundary layer has been characterized in terms of generated instabilities