The major obstacle to eradicating HIV-1 is the ability of integrated, replication competent viral DNA to persist latently in cellular reservoirs. Despite there being a significant and extensive knowledge base regarding HIV-1 infection of the CNS and the development of neurological disorders in HIV-1 infected viremic individuals, there is only a very limited understanding of the mechanisms of persistence in the CNS following viral suppression. Despite significant indirect data supporting the CNS as a potential reservoir of HIV-1 in virally suppressed individuals, there remains critical gaps in our knowledge regarding the location, frequency and nature of viral persistence in the CNS. This data is critical to both developing strategies aimed at the development of both a functional or sterilising cure. To characterise the persistent reservoir of HIV in the CNS specifically the frequency and type of persistently infected cells and the nature of the persistent virus, we have developed highly specific and sensitive in situ hybridisation techniques (RNAScope/DNAScope and BaseScope), coupled with laser capture microdissection and highly sensitive PCR. The application of these techniques to CNS reservoirs and tissue analysis more broadly will be discussed.