Lipidomics is a rapidly growing technology that can be used in biomedical research to study disease mechanisms, identify novel disease biomarkers and drug efficacy biomarkers, and reveal off-target effects. Lipidomics can also be used to elucidate the mechanism of action of different drug compounds or as readouts in Mendelian randomization approaches. Furthermore, lipidomics can be utilized to identify deviations in metabolic and/or signaling pathways in different stages of disease. Therefore, as we discuss here, this emerging technology also has a substantial potential in various drug discovery programs.