This study used an integrated approach to investigate pegmatite areas in eastern Afghanistan. The analysis of surface data, including a digital elevation model (DEM), and Landsat Enhanced Thematic Mapper Plus (ETM+) images, was combined with airborne magnetic data to better understand three-dimensional geology in the area. The ETM+ and DEM data were used to map geological structures at the surface, which indicate that the area consists of two main fault systems that trend NNE and E-W. The two trends represent the remnants of reactivated structures that formed under the stress regimes generated during the tectonic evolution of eastern Afghanistan. Magnetic data indicate an NE-SW trending basin. A two-dimensional schematic model shows that the basin gradually deepens toward the SW with depths to the magnetic basement ranging between 2 and 11.5 km. The integration of the results gave new insight into the tectonic evolution and structure patterns near the pegmatites area.