Display omitted •PLR and PTR decreased low-density lipoprotein cholesterol levels in patients with mild dyslipidemia during the follow-up, but the reductions were not significantly greater than the placebo.•High-density lipoprotein cholesterol levels significantly increased after PLR treatment than after the placebo, whereas this effect was not observed for PTR.•Both PLR and PTR were tolerable up to three months’ treatment. This randomized, double-blind trial assessed the efficacy and safety of Pueraria lobata radix (PLR) and Pueraria thomsonii radix (PTR) for dyslipidemia. We randomly assigned 174 patients with mildly elevated low-density lipoprotein cholesterol (LDL-C) levels to receive 15 g/day PLR, PTR, or a placebo for 12 weeks. Changes in baseline LDL-C levels after PLR or PTR treatments compared with placebo treatment were not significant. High-density lipoprotein cholesterol (HDL-C) levels increased more significantly after PLR treatment than placebo treatment (+3.05 mg/dl, 95 % confidence interval = 0.75–5.35), whereas this effect was not observed for PTR treatment. Regarding PLR treatment, increases in HDL-C levels were mainly observed in the female, >50 years old, and nondrinker subgroups. The treatments did not show significant effects on other outcomes. No PLR- or PTR-related adverse events were reported. Given its effect on HDL-C, daily consumption of PLR, but not PTR, may represent an edible, medicinal remedy to manage dyslipidemia.