Three dimensional flow separation occurring in a vaneless diffuser at small flow rates was analyzed by using the numerical simulation with the low Reynolds-number turbulence model (LRN k-ε) as well as the momentum integral method (MI). Comparison between the LRN k-ε calculation and the experiment indicates quite a good agreement in the 3-D boundary layer velocity profile. The numerical investigation shows that the LRN k-εcalculation can predict the reverse flow in the vaneless diffuser, while the MI-method behaves relatively poor although it captures the overall flow pattern correctly. It is clarified that a small gradient in the inlet tangential velocity distribution with respect to the diffuser depth is the key factor which dominates the reverse flow behavior in the vaneless diffuser at small flow rates, as demonstrated in the experiment.