In this study, the marker compound contents of both the taproot and lateral root of Danshen (Salvia miltiorrhiza Radix), which is cultivated in Korea, were investigated. The salvianolic acid B content was the highest in the taproot (5.17-6.75%) and lateral root (3.99-5.69%). The cryptotanshinone, tanshinone I, and tanshinone IIA contents were higher in the lateral root than in the taproot of Danshen (p <0.05). Principal component analysis results revealed that the taproot was correlated to the salvianic acid A, rosmarinic acid, salvianolic acid B, and salvianolic acid A contents, whereas the lateral root was correlated to the cryptotanshinone, tanshinone I, and tanshinone IIA contents. The total phenolic content and total flavonoid content of the taproot were higher than those of the lateral root (p <0.05); however, the antioxidant activities of the taproot and lateral root of Danshen were similar. The salvianolic acid B content was correlated to the TPC of the taproot (r=0.748) and the 2,2-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid radical scavenging activity of the lateral root (r=0.847). This study could provide useful information for the classification of Danshen as a herbal medicinal product.