Conjugated linolenic acid (CLNA) is a mixture of positional and geometric isomers of octadecatrienoic acid (α-linolenic acid, cis9,cis12,cis15-18:3 n-3) found in plant seeds. Three 8,10,12-18:3 isomers and four 9,11,13-18:3 isomers have been reported to occur naturally. CLNA isomers such as punicic acid, α-eleostearic acid and jacaric acid have been attributed to exhibit several health benefits that are largely based on animal and in vitro studies. This review has summarized and updated the evidence regarding the metabolism and bioactivities of CLNA isomers, and comprehensively discussed the recent studies on the effects of anti-carcinogenic, lipid metabolism regulation, anti-inflammatory, anti-obese and antioxidant activities of CLNA isomers. The available results may provide a potential application for CLNA isomers from natural sources, especially edible plant seeds, as effective functional food ingredients and dietary supplements for the above mentioned disease management. Further research, especially human randomized clinical trials, is warranted to investigate the detailed physiological effects, bioactivity and molecular mechanism of CLNA.