Because HIV is a fast-evolving virus, HIV genomic sequences of several individuals can be used to investigate whether they belong to a transmission network. Since the infamous 'Florida dentist case' in the beginning of the 1990s, phylogenetic analyses has been recurrently used in court settings as a forensic tool in HIV transmission investigations, for example cases where one or more complainants allege that a defendant has unlawfully infected them with HIV. Such cases can arise both in the context of HIV-specific criminal laws - in countries where transmission of HIV infection is specifically criminalized - or in the context of general laws, for example, by applying physical or sexual assault laws to HIV-related cases. Although phylogenetic analysis as a forensic technique for HIV transmission investigations has become common in several countries, the methodologies have not yet been standardized, sometimes giving rise to unwarranted conclusions. In this literature review, we revisit HIV court case investigations published in the scientific literature, as well as the methodological aspects important for the application and standardization of phylogenetic analyses methods as a forensic tool. Phylogenetic methodologies are improving quickly, such that more recently, phylogenetic relatedness, directionality of transmission and timing of nodes in the tree are used to assess whether the phylogenetic transmission analysis is consistent with or contradicting the charges. We find that there has been a lack of consistency between methods used in court case investigations and that it is essential to define guidelines to be used by phylogenetic forensic experts in HIV transmission cases in court.