The ATLAS reconstruction of charged particle trajectories relies on the Inner Detector tracking system. The accuracy of the reconstruction is limited by the finite resolution of the detector elements and the imperfect knowledge about their positions. A precise alignment of the detector is therefore essential. Here, the strategy and the status of the Inner Detector alignment in ATLAS during the LHC Run 2 are presented and the alignment challenges related to the distortion of the new innermost Pixel layer, the IBL, are discussed.