A direct numerical simulation of a three dimensional diffuser at Reynoldsnumber Re = 10, 000 (based on inlet bulk velocity) has been per-formed using a low-dissipation finite element code. The geometry chosenfor this work is the Stanford diffuser, introduced by Cherry et al.(Int.J. Heat Fluid Fl. 29, 2008, pp. 803-811). Results have been exhaus-tively compared with the published data with a quite good agreement.A proper orthogonal decomposition and a dynamic mode decompositionanalysis of the main flow variables have been performed to identify themain characteristics of the large-scale motions. A combined motion of thelarge-scales has been found to originate in the top-right expansion cornerwith two clear features. A low-frequency diagonal cross-stream beatingfeature first reported by Malm et al. (J. Fluid Mech. 699, 2012, pp.320-351), has been clearly identified in the spatial modes of the stream-wise velocity components and the pressure, associated with the narrowband frequency of St ∈ [0.083, 0.01]. This feature has been found tobe more compacted near the expansion corner and elongates inside the diffuser section. A second low-frequency feature has been identified asso-ciated with the secondary flows and acting as a back and forth globalaccelerating-decelerating motion on the diffuser. The frequencies associ-ated to this motion are of St < 0.005, while the smallest observed inthis work has been St = 0.0013. This low-frequency motion observedin the Stanford diffuser point out the need for longer simulations.