Less costly but still accurate methods for monitoring HIV treatment response are needed. We prospectively evaluated if a qualitative polymerase chain reaction (PCR) amplification assay for virologic monitoring could maintain accuracy while reducing costs in Seoul, South Korea. We conducted the first prospective study comparing a qualitative PCR amplification of HIV-1 reverse transcriptase (RT) versus a commercial real time PCR assay (i.e. viral load) for virologic monitoring of 150 patients receiving antiretroviral therapy (ART) between November 2011 and August 2012 at an urban hospital in Seoul, South Korea. A total of 215 blood plasma samples from 150 patients receiving ART for more than 6 months were evaluated. Using the individual viral load assay, 12 of 215 (5.6%) plasma samples had more than 500 HIV RNAcopies/mL. The qualitative PCR amplification assay detected individual samples with ≥ 500 HIV RNA copies/mL with 100% sensitivity. The specificities of the qualitative PCR amplification of HIV-1 RT assay were 94.1%, 93.6%, and 93.2% compared to the real time PCR at 500, 1000, and 5000 threshold of HIV RNA copies/mL, respectively, and $24,940 USD would have been saved for 150 patients during 10 months. The qualitative PCR amplification of HIV-1 RT assay might be a useful approach to effectively monitor patients receiving ART and save resources.