During the last two decades the realization has emerged that the phenotype of the majority of inherited genetic diseases, including inborn errors of metabolism, cannot be predicted by the genotype identified in patients. This is true for PKU and in the majority of fatty acid oxidation (FAO) defects, where the genotypes identified in patients may be allocated into two groups. One comprising big deletions and small out-of-frame deletions/insertions as well as severe splice and stop codon changes, generally giving rise to no or very little protein product, and the other group, comprising small in-frame deletions/insertions and missense variations, resulting in misfolding proteins with varying stability. In all cases of FAO defects the pathophysiology may be due to energy insufficiency as well as toxic effects from accumulated enzyme substrates. In patients carrying missense variations, it may in addition be caused by the presence of misfolding proteins. A common effect of accumulated substrates and misfolding proteins is chronic oxidative stress, the severeness of which may depend on a complex interplay of modifying factors, including genetic, cellular, environmental and dietary. In this review we will discuss the hypothesis that especially the amounts of reactive oxygen species (ROS) and reactive nitrogen species (RNS), created in connection with the electron transport chain (ETC), are the driving forces in the balance between cell survival and death. In young and healthy cells small amounts of ROS function as signaling molecules, activating cell protection systems, such as protein quality networks, antioxidant enzymes and metabolic shift from ATP production by the ETC to glycolysis. In the sick and old cell, containing misfolding and damaged proteins, the dynamic range of these protecting systems are narrowed, and cells develop a state of chronic stress, which easier than young and healthy cells may initiate cell death programs like apoptosis and necrosis. We will discuss a wealth of literature that support this hypothesis, which - if supported by studies - is important for new treatment strategies. We conclude that crude antioxidant treatment may not be beneficial, since it may inhibit the survival stress responses. We discuss the ongoing studies to enhance the residual activity of mild misfolding enzyme proteins by cofactor or chemical chaperones or by inducing the transcription of FAO enzyme proteins by bezafibrate with respect to misfolding/distorted conformational proteins ability to create ROS, and the need to know the exact pathophysiological mechanisms in order to suggest new treatment regimes., (© 2013.)