Background: All human immunodeficiency virus (HIV -1) uses a host tRNA Lys,3 as the primer for reverse transcription. The tRNA Lys,3 is bound to a region on the HIV-1 genome, the primerbinding site (PBS), that is complementary to the 18 terminal nucleotides of tRNA Lys,3. How HIV-1 selects the tRNA from the intracellular milieu is unresolved. Results: HIV-1 tRNA primer selection has been investigated using viruses in which the primerbinding site (PBS) and a sequence within U5 were altered so as to be complementary to tRNAMet, tRNAPro or tRNAIle. Analysis of the replication of these viruses in human peripheral blood mononuclear cells (PBMC) revealed preferences for the selection of certain tRNAs. HIV-1 with the PBS altered to be complementary to tRNAMet, with and without the additional mutation in U5 to be complementary to the anticodon of tRNAMet, stably maintains the PBS complementary to tRNAMet following extended in vitro culture in PBMC. In contrast, viruses with either the PBS or PBS and U5 mutated to be complementary to tRNAIle were unstable during in vitro replication in PBMC and reverted to utilize tRNALys,3. Viruses with the PBS altered to be complementary to tRNAPro replicated in PBMC but reverted to use tRNALys,3; viruses with mutations in both the U5 and PBS complementary to tRNAPro maintained this PBS, yet replicated poorly in PBMC. Conclusions: The results of these studies demonstrate that HIV-1 has preferences for selection of certain tRNAs for high-level replication in PBMC. © 2005 Moore-Rigdon et al., licensee BioMed Central Ltd.