Dysfunctions of mitochondrial fatty acid beta-oxidation (beta-FAO) in various tissues represent a hallmark of many common disorders, and are acknowledged to play an essential role in the pathogenesis of diabetes, obesity, and cardiac diseases. Moreover, inborn defects in beta-FAO form a large family of rare diseases with variable phenotypes, ranging from fatal multi-organ failure in the newborn to isolated adult onset myopathy. These pathologies highlight the critical role of beta-FAO in many tissues with high-energy demand (heart, muscle, liver, kidney). Furthermore, and unexpectedly, very recent data unveiled the possible involvement of beta-FAO in instructing complex non energy-related functions, such as chromatin modification, control of neural stem cell activity, or survival and fate of cancer cells. Pharmacological targeting of beta-FAO by small molecules might therefore open new avenues for the treatment of various rare or common diseases.