Extracts from the root of Lithospermum erythrorhizon (gromwell) have been used for many centuries as a natural red dye and crude drugs with excellent performance for wound healing. In particular, shikonin a major constituent of the gromwell colorant is reported to possess antibacterial, antioxidant, anti-inflammatory, antitumor activities, etc. Therefore, we tried to manufacture antimicrobial and antioxidant cotton fabrics for biocompatible clothing materials using the natural stuff and environmentally friendly process. In this study, cotton fabrics were dyed with the colorant extracted from the root of gromwell, and their properties were closely investigated. Consequently, we discovered that the cotton fabrics dyed with the extracts from the root of gromwell showed excellent antioxidant performance as well as antibacterial ability. Also, the functionalities and color fastness were improved by gallnut mordanting and cationization of the cotton fabrics.