In the first part of this project, methods to characterise the cellular tropism of HIV were investigated. A novel vector was produced which could be used to generate recombinant HIV that express study subject-derived envelope (env) glycoproteins. The vector incorporated the enhanced green fluorescent protein (EGFP) gene to allow easy identification of infected cells. Three methods for production of chimeric virus without the need to amplify the full genome in E. coli were designed. All methods were capable of producing infectious virus expressing various env genes. The second part of the project sought to investigate the distribution of drug resistance variants in vivo. DNA was extracted from post mortem brain and lymphoid tissues from HIV infected study subjects. Limiting dilution PCR was used to obtain PCR products each derived from a single proviral template molecule. No differences were found in the distribution of drug-resistance mutations between the two compartments for three out of four study subjects. In the final part of the project, a method for the bulk isolation of microglia and astrocytes form post-mortem HIV-infected brains was optimised. FACS sorting was carried out using CD68 and GFAP as markers of microglia and astrocytes respectively. Separation of cells was carried out using two HIV-infected brains. No provirus was detected in the separated cells however the brain material used was from asymptomatic study subjects and had extremely low proviral loads. It is hoped that in the future the technique could be used to separate brain material which has a higher proviral load thereby allowing quantification of the level of HIV infection of these two cell types.