Sea cucumbers are important sources of human food and pharmacological compounds. However, few studies have evaluated the potential differences between the sexes or organs in a particular species to explore new commercial opportunities. In this study, the proximate composition and amino acid profile of the body wall, the saponin content in the organs of Athyonidium chilensis males and females, and their cytotoxicity against colon cancer cells were evaluated. There were no significant differences in the proximate composition and amino acid profile of the body wall between the sexes. Protein content differed significantly between organs and sexes, fluctuating between 36.29 % and 72.98 % (dry weight). Saponin content was significantly higher in the gonads and lower in the longitudinal musculature. Cell viability was significantly lower (9.50 ± 2.23 %) with the digestive system saponin extract than with 40 % (94.75 ± 2.65 %). This work demonstrates the great potential of A. chilensis as a food and source of saponins with pharmacological importance.