For ideal clinical benefit, human immunodeficiency virus (HIV)-infected individuals should receive continuous medication. This is the first nationwide antiretroviral therapy (ART) adherence study in Asia, where medication monitoring at national level is systemically available. We estimated the ART adherence of incident HIV-infected individuals and investigated factors affecting low medication adherence using the national health insurance (NHI) claims data from 2007 to 2016. Medication possession ratio (MPR) was used to measure medication adherence and risk factors were identified by multivariable logistic regression analysis. Of the 8,501 newly diagnosed HIV-infected individuals during 2009â2016 with at least one ART prescription, 70.4% of HIV patients had adequate adherence to ART defined as MPR â„95%. Requiring prophylactic antibiotics, female gender, age of 0â19 and same or over 50âs compared to 30â39, and having a history of malignancy, lower socioeconomic status, not visiting tertiary hospital, and being diagnosed in the earlier years were risk factors for lower adherence (Odds ratio 1.7, 1.6, 1.6, 1.4, 1.6, 2.1, 1.2, and 1.6 to 3.8 respectively). Health authority should take into consideration of these modifiable and unmodifiable barriers to establish sustainable monitoring system at national level and to improve adherence.