Antioxidant activities of minor pigments of sea urchins (1-5) and synthetic naphthazarins (7-13) were evaluated and compared with echinochrome A (6) using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) scavenging assays. Structure-activity relationships showed that the antioxidant activities of the tested compounds depended on the number and positions of hydroxyl groups. Compounds bearing 3 or 2 hydroxyl groups on a naphthazarin core (5,8-dihydroxy-1,4-naphthoquinone) were the most active in both assays. Echinochrome A (6) (IC50 7.0 microM) and its monomethyl ethers 7 (IC50 15.0 microM) and 8 (IC50 15.0 microM) displayed stronger activities than Trolox (IC50 16.0 microM) in the DPPH and ABTS assays (TE = 3.41, 2.35, and 2.35 mM, respectively). Compounds with either one or without hydroxyl groups on a naphthazarin core displayed activities significantly lower than Trolox in both assays. These results suggest that hydroxylated naphthazarin pigments of sea urchins have a potential use as natural antioxidants.