In the current study, we conducted petrographic investigation combined with aeromagnetic data in order to classify variable granitic rocks, delineate structural trends and deduce depth of the basement rocks cropping out in Homrit Waggat area, Central Eastern Desert, Egypt. Field and petrographic investigations revealed that the granitic Homrit Waggat rocks include two groups. The first group includes the older granitic rocks, comprising tonalites and granodiorites. In contrast, the second one includes younger granitic rocks, involving alkali-feldspar granites, syenogranites and albitized granites. Depth as well as subsurface structures can be identified using magnetic method. Two tectonic maps representing the deep-seated and the shallow-seated structural features were constructed to show the structural history of the study area. The major tectonic trends indicate that the regional structures are controlled by deeper structures which have NW–SE, NNE–SSW—NE–SW and N–S directions. On the other hand, we find that the local structure trends are controlled by the local shallow structures that have NNE–SSW, NNW–SSE, ESE–WNW and N–S directions. Depth levels of the economic rare metal-bearing rocks range from 0 km to 1.2 km (Euler deconvolution technique) and from 0 km to 2.3 km (the analytical signal profiles) by using the aeromagnetic data, reflecting large resources of rare metal-bearing rocks.