We integrated Shuttle Radar Topography Mission (SRTM) Digital Elevation Models (DEM), airborne magnetic, radiometric and three-dimensional Full Tensor Gravity Gradiometry (3D-FTG) data to investigate the role of Precambrian structures in the evolution of the largely amagmatic Miocene-Recent aged Albertine and Rhino grabens in Uganda. These grabens represent the northern segment of the Western Branch of the East African Rift System (EARS). The two NE-trending grabens are connected by a right-stepping transfer zone and they extend within the Archean-Paleoproterozoic Northeast Congo block which represents the northeastern extension of the Congo craton. Our results show the following and highlight the importance of pre-existing structures in the evolution of continental rift systems: (1) The NE-extent of the Albertine full-graben is controlled by NE-trending Precambrian fabric and the graben terminates at its northeastern end when it encounters a multiply folded Precambrian basement terrain with poorly-developed NW-trending structural grain. Additionally, the northeastern termination of the Albertine graben coincides with the presence of NW-trending right-stepping high-density bodies within the Precambrian terrain. (2) The transfer zone between the Albertine and Rhino grabens is controlled by NE-trending Precambrian structures which might have facilitated the development of relay ramp faults. (3) Strain localization within the better-developed southeastern border fault of the Rhino half-graben is facilitated by the presence of Precambrian structures better aligned in a NE-direction in the southeastern part of the basin compared to its northwestern part. (4) Further to the northeast, the Rhino graben is segmented and transitions into a narrower ENE-trending half-graben with a better-developed border fault on its northwestern side. This segmentation coincides with the presence of N-trending Precambrian structures. (5) The Rhino graben terminates farther northeast against the NW-trending Precambrian Aswa shear zone; a prominent structure with complex, but generally NW-trending fabric.