The human immunodeficiency virus (HIV) is present in several sites inside the human body, which are hardly accessible to antiretroviral drugs, the so-called sanctuary sites. The most important sanctuary sites are cerebrospinal fluid (CSF), peripheral blood mononuclear cells (PBMCs) and seminal plasma. The determination of drug concentrations in these sanctuary sites may form an important step in treatment optimisation of HIV-infected individuals. However, bioanalysis in these sites is hampered by several factors with regard to sample preparation, chromatography and detection. In this review, we will discuss these issues and give an overview of published methods using high-performance liquid chromatography (HPLC) for the bioanalysis of HIV protease inhibitors in CSF, PBMCs and seminal plasma.