It has been assumed that R5 and X4 HIV utilize similar strategies to support viral cDNA synthesis post-viral entry. In this study, we provide evidence to show that R5 and X4 HIV have distinct requirements for host cell uracil DNA glycosylase (UNG2) during the early stage of infection. UNG2 has been previously implicated in HIV infection, but its precise role remains controversial. In this study we show that although UNG2 is highly expressed in different cell lines, UNG2 levels are low in the natural host cells of HIV. siRNA knockdown of endogenous UNG2 in primary cells showed that UNG2 is required for R5 but not X4 HIV infection, and that this requirement is bypassed when HIV enters the target cell via VSV-G mediated endocytosis. We also show that siRNA knock down of UNG2 in virus producing primary cells leads to defective R5 HIV virions that are unable to complete viral cDNA synthesis. Quantitative PCR analysis revealed that endogenous UNG2 levels are transiently up-regulated post-HIV infection, and this increase in UNG2 mRNA is approximately 10-20 times higher in R5 verses X4 HIV infected cells. Our data show that both virion-associated UNG2 and HIV infection induced UNG2 expression are critical for reverse transcription during R5 but not X4 HIV infection. More importantly, we have made the novel observation that R5 and X4 HIV have distinct host cell factor requirements and differential capacities to induce gene expression during the early stages of infection. These differences may result from activation of distinct signalling cascades and/or infection of divergent T-lymphocyte subpopulations.