This study was conducted to monitor residual pesticides in ginseng and balloon flower roots and to assess their risk to human health. All of 112 samples consisted of ginseng and balloon roots were purchased from traditional domestic markets and supermarkets in nine provinces of Korea in 2012. Multi-residue analysis of 122 pesticides was conducted and the analysis was performed by gas chromatography-electron capture detector, gas chromatography- nitrogen/phosphorus detector, and high-performance liquid chromatography. Seven pesticides were detected in 12 root samples and the detection rate was 10.7%. The detected twelve root samples were 10 ginseng root samples and 2 balloon root samples. Pesticides detected in root samples were procymidone, kresoxim-methyl, endosulfan, cypermethrin, tralomethrin, tetraconazole and chlorfluazuron. Among them, two pesticides as tetraconazole in a balloon flower root and cypermethrin in a ginseng root exceeded the recommended maximum residue limit set by Korea Food and Drug Administration. Five pesticides detected from 10 root samples were identified as unregistered pesticides in Korea. In order to do risk assessment with Korean medicinal plant consumption, estimated daily intake of residual pesticides were determined and compared to acceptable daily intake, referring to %ADI values. The range of %ADI values was from 0.006% to 0.333%. Taken together, it demonstrates the pesticides found in the two root samples were below the safety margin, indicating no effect on human health.