Highly active antiretroviral therapy (HAART) is the common treatment strategy for human immunodeficiency virus (HIV)-infected patients at present. Generally, HAART regimens apply multi-therapy drugs that contain nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs), non-nucleoside/nucleotide reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs). Unlike NNRTIs and PIs, the active form of NRTIs is not the drug itself but its triphosphorylated (TP) metabolites in intracellular medium. Analysis of both the prodrugs or NRTIs and their intracellular metabolites is needed to provide overall information in pharmacokinetic and therapeutic effects to HIV-infected patients. Numerous publications have reported the assays for NRTIs and their phosphorylated metabolites in various biological matrices. The methods involved liquid chromatography (LC) with UV detection (LC-UV), LC with tandem mass spectrometry (LC-MS/MS), capillary electrophoresis/electrochromatography (CE/CEC) with UV detection (CE/CEC-UV) or/and MS/MS detection (CE-MS/MS). Due to the extremely low concentration of NRTIs and the phosphorylated metabolites as well as the complex biological matrices, sample pretreatment methods such as protein precipitation (PP), liquid-liquid extraction (LLE) and solid-phase extraction (SPE) have played important role in the successful analytical method development.