Currently, raltegravir is the only approved integrase inhibitor that targets the integration stage of the HIV-1 lifecycle. The clinical manifestations of raltegravir-related potential adverse effects on V(D)J recombination may be so rare that they may only be observed after large numbers of patients are exposed to this drug. Evaluating the direct in vivo interaction of HIV integrase inhibitors on RAG-1/2 is difficult, therefore the best approach may be to evaluate the potential negative effects on recombinase activity downstream by studying immune function. If gene rearrangements of immunoglobulin and T-cell receptor genes are altered by HIV integrase, then patient lymphocytes will fail to display normal responses to neo-antigen exposure. Since untreated HIV-infected individuals have an impaired ability to respond to new antigens, it is difficult to evaluate the responses to neo-antigens in these individuals. Therefore, to test this hypothesis, it would be best to choose patients with long-term control of HIV that have recovered immune function.