The Kutai basin, East Kalimantan, is one of several large extensional basins formed in the Middle to Late Eocene. Formed above an orogenic complex of Late Cretaceous/Early Tertiary age, basement fabrics oriented NW–SE and NE–SW strongly influenced basin extension and inversion. Remote sensing data and fieldwork show basement fabric on the margins and Tertiary cover are dominated by NE–SW, NW–SE and NNE–SSW-trending structures. Similarly, on a larger scale, NW–SE narrow linear gravity lows cut NNE–SSW highs on the gravity data within the basin. Reconstruction of the basin architecture shows NNE–SSW basin-bounding faults overlapping in a right stepping en-echelon manner. These overlaps (relay ramps) were breached by faults oriented NE–SW through reactivation of the basement fabric. Opposing antithetic and synthetic half-grabens were linked by highly oblique NW-SE transfer faults. Inversion utilized extensional faults as reverse faults; however, NW–SE-oriented structures were reactivated as zones of lateral offset along the fold-thrust belt, whilst fault kinks oriented NE–SW were reactivated as oblique-slip reverse faults. The Kutai Basin provides an example of the controls that basement heterogeneities play on both extension and inversion.