The purpose of this contribution is to evaluate the cytotoxicity and apoptosis inducing ability of structurally diverse anthraquinones to establish a relationship between structure and toxicity. Besides the wide spread use of anthraquinones in pharmacological drugs for constipation and non-prescription dietary supplements for weight loss, extracts are still commercialized as crude extracts and long-term side effects are still relevant. In this work we developed a method to quantify the cascarosides isolated from Rhamnus purshiana (Cascara Sagrada) using LC-MS/MS and evaluated the effects of this extract and isolated compounds on cellular viability using NOK-SI, HeLa, and T98G cell lineages. Apoptosis inducing ability was also analyzed via evaluating key-proteins involved in apoptosis pathways. Using cascarosides isolated from bark extracts, we found that the presence of glucose moieties in the chemical structure reduced the toxicity. This communication reviewed the mechanisms of action, toxicity of anthraquinones and correlated the toxicity with chemical structures of cascarosides. Results indicate that cascarosides-enriched cascara extract, as well as glycosylated anthraquinones, may have some beneficial effects for laxative action of herbal medicines. Considering our results, a cascarosides-enrichment in cascara extract is recommended.