Quinones and quinone imines are highly reactive metabolites (RMs) able to induce dangerous effects in vivo. They are responsible for all kinds of toxicity, for example, cytotoxicity, immunotoxicity, and carcinogenesis. Furthermore, hepatotoxicity of chemicals/drugs in particular can be induced by quinone and quinone imine metabolites. According to their reactivity, quinones and quinone imines react as Michael's acceptors with cell proteins or DNA and, in this way, cause damage to the cells. Quinones and quinone imines also have high redox potential and, due to their semiquinone radicals, are capable of redox cycling and forming reactive oxygen species (ROS). However, the presence of quinones and quinone imines structures in compounds is not always responsible for a toxic effect. The main question, therefore, is what are the main factors responsible for the toxicity of the chemicals and drugs that form RMs. For this reason, the presence of structural alerts and evidence for the formation of reactive quinones and quinone imines metabolites and their mechanisms of toxicity through cellular effects are discussed in this review, together with examples.