We report an ab initio study of the semiconducting Mg2X (with X = Si, Ge) compounds and in particular we analyze the formation energies of the different point defects with the aim of understanding the intrinsic doping mechanisms. We find that the formation energy of Mg2Ge is 50% larger than that of Mg2Si, in agreement with the experimental tendency. From a study of the stability and the electronic properties of the most stable defects, taking into account the growth conditions, we show that the main cause of the n doping in these materials comes from interstitial magnesium defects. Conversely, since other defects acting like acceptors such as Mg vacancies or multivacancies are more stable in Mg2Ge than in Mg2Si, this explains why Mg2Ge can be of n or p type, in contrast to Mg2Si. The finding that the most stable defects are different in Mg2Si and Mg2Ge and depend on the growth conditions is important and must be taken into account in the search for the optimal doping to improve the thermoelectric properties of these materials.