Deep X-ray surveys provide unprecedented access to the population of accreting super-massive black holes (SMBH) at high redshift. I will present our recent results (Vito et al. 2018) on the 3<z<6 AGN population in the 7 Ms CDF-S and 2 Ms CDF-N, the deepest X-ray surveys to date. We put tight constraints on quantities such as the obscured AGN fraction and the number density of z>3 AGN. I will show our findings on the high-redshift AGN X-ray luminosity function, focussing in particular on the slope of the faint end, accessible only by the deepest X-ray surveys. This is particularly important to assess the contribution of AGN to the cosmic reionization. All of these results will be placed in the context of SMBH seeds formation and growth. I will also discuss how future missions like Lynx, Athena and JWST will boost our knowledge of the SMBH formation and evolution in the early Universe.