In the present study, we investigated whether a gross deletion in the nef gene (g∆nef) is induced by Korean red ginseng (KRG) intake. Ten patients were treated with KRG powder for 3 years in the absence of antiretroviral drug therapy. On average, 3,555 ± 1,042 g KRG was administered per person over 36.1±2.4 months. There was a mild decrease in CD4 T cell count (75 ± 110/mL) over the 36.1±2.4 months (p = 0.059). We obtained 355 nef amplicons using 71 peripheral blood mononuclear cell samples over a 3-year period. All ten patients exhibited g∆nef (range, 3.2 to 45.9%). At baseline, 3 of 78 amplicons (3.8%) exhibited g∆nef, whereas 18.8% (52/277) revealed g∆nef during KRG-intake (p < 0.001). The proportion of g∆nef was significantly correlated with monthly dose of KRG (r = 0.89, p < 0.001). The median time for first detection of g∆nef was 13 months. In conclusion, our data show that g∆nef is inducible by KRG intake and its proportion is dependent on the duration of KRG intake and dose of KRG.