In the literature it is proven that thermal vacancies have a great influence on the mechanism of hardening of Fe-Al alloys. Moreover, in these alloys, we observed a long-range ordering, which can significantly affect the mechanical and physical properties and their stability. In this paper, influence of low-temperature annealing on elimination of excess vacancies was investigated. TEM observation of annealed specimens for the alloys with 28 and 38 at.% aluminum have helped elucidate the phenomena responsible for vacancies elimination due to the occurrence of particular interactions between point and linear structure defects. It was shown that the aluminum content influences significantly changes in defects structure. The alloy with 28 at.% aluminum has mainly superdislocations in the structure, while in alloy with 38 at.% aluminum, mainly unit dislocations and high-energy dislocation configurations, like dislocation loops, dislocation dipoles, and dislocation jogs, were observed. The results suggest that different defect types may control the diffusion process during low-temperature annealing and that it is affected by alloy composition.