After the infusion of HIV-1 virus into a host cell, RNA is reverse transcribed to dsDNA, which persists intracellular to the infected cell in a variety of forms. Numerous in-house assays have been developed for the quantification of the different cellular HIV-1 DNA forms; these implement conventional or real-time PCR methodology. In this review we discuss recent findings about the longitudinal monitoring of cell-associated HIV-1 DNA in naïve and pre-treated patients, as a marker for clinical progression, treatment initiation and long-term success of HAART. These findings underline the importance of monitoring HIV-1 DNA in clinical practice, in addition to HIV-RNA and CD4(+) T Cell counts, for the better assessment of HIV-treatment and disease progression. The lack of a standardized real-time PCR assay is major impediment to more wide-spread HIV-1 DNA monitoring.