Computational fluid dynamics analysis of the complex flows in a cryogenic turboexpander is essential for any improvement in its performance. This includes a detailed analysis of the unsteady turbulent flows imparted mainly by the rotor stator interactions. The flow unsteadiness due to rotor stator interaction is caused by the relative motion between the stationary and rotating component, interaction of the turbine wheel blades with the wakes and vortices generated by the upstream blades and at trailing edges. In order to minimize the loss generation due to this unsteadiness, the vaneless space length at the nozzle-Turbine wheel interface and the length of the straightening portion at the turbine wheel-diffuser interface should be optimised considering the mechanical constraints. In this paper three dimensional unsteady viscous flow analysis of a helium cryogenic turboexpander was carried out using Ansys CFX to investigate the origin and flow mechanisms that cause these unsteady phenomena. The analysis has been done for three different lengths of straightening duct at the turbine wheel diffuser interface. The performance parameters from the computational results were compared and analysed to understand the flow characteristics in each case. Copyright © 2016 by ASME.