Gene therapy offers a potentially an effective treatment for many human diseases, including HIV/AIDS. One of the most studied gene delivery systems is the use of lentivirus based vectors, which can deliver genes into both dividing and nondividing cells. However, low infection efficiency represents an obstacle for proper evaluation of their biological function. In this study, a recombinant lentiviral vector which expressed short hairpin RNAs (shRNAs) targeted against the HIV-1 vif/pol was transduced into various cells. An MHC class I molecule, H-2K(k), was used as a marker to accumulate the virally transduced cells through immunomagnetic sorting. In vitro testing of transduced cells showed 85% suppression of HIV in post-sorted PBMCs compared to 30% in pre-sorted PBMCs. In additional, using a mouse xenotransplantation model with the same treatment protocol for cell enrichment, a >95% decrease in HIV activity in post-sorted cells was achieved, as compared to nearly none in the pre-sorted cells. These studies offer a practical method to accumulate virally transduced cells, which can be applied to evaluate the performance of various shRNAs constructs.