Abstract. The inner detector of the ATLAS experiment is in the process of being commissioned using cosmic ray events, first at the surface and then together with the other subdetectors in the ATLAS cavern. The full software chain has been set up in order to reconstruct and analyse this kind of events. Final detector decoders have been developed, pattern recognition algorithms and track fitters have been validated as well as the various alignment and calibration methods. The infrastructure to deal with conditions data coming from the data acquisition, detector control system and calibration runs has been put in place, allowing also to apply alignment and calibration constants. The software has also been essential to monitor the detector performance during data taking. Detector efficiencies, noise occupancies and resolutions have been studied in detail and compared with those obtained from simulation.