Because plants are static and live in a competitive and sometimes hostile environment, they have evolved efficient mechanisms that protect them from abiotic and biotic stresses. These mechanisms include detoxification and sequestration of xenobiotic compounds and of toxic trace elements, exploited in any phytoremediation process. However there must be a limit on the amount of pollutants that can be accumulated and detoxified without disrupting the normal plant biochemistry and physiology. This limit seems to depend not only on plant species, but also on the ecotype or cultivar. The presentation aims to highlight some biochemical mechanisms, suggested or supposed to of importance for the successful phytoremediation of organic contaminants. Enzymes involved in xenobiotics detoxification are often linked to the redox chemistry of the cell. The activities of cytochrome P450 monooxygenase, peroxidase and glutathione transferase have implications on the regulation of cellular redox status, closely related to mitochondrial respiratory chains, also involved in maintaining the cellular and plant energy balance and carbon flow. For example, overloading a plant with high concentrations of xenobiotics requiring oxidation by P450 may compete with the normal functions of these enzymes. An increase in their activity may also impose a major demand on both intracellular O2 and NAD(P)H pools, disturbing plant redox or energy status, and thus affecting both primary and energy metabolism. Plant mitochondrial respiratory chains differ from the mammalian one. In addition to Complex I, they contain at least four other dehydrogenases that enable the controlled oxidation of matrix and cytoplasmic NAD(P)H. Furthermore, plant mitochondria are characterized by the presence of an alternative respiratory pathway, through which reducing equivalents can be transferred to oxygen. This pathway branches at the level of the ubiquinone pool and comprises a single enzyme, the alternative oxidase, not coupled to the synthesis of ATP and insensitive to cyanide. Increase in the expression and/or activity of the alternative oxidase has been observed during temporal events such as seed conditioning, leaf development, elevation of salicylic acid levels, thermogenesis, fruit ripening, oxidative stress, physical wounding and plant pathogenic attack. The alternative pathway is inhibited by benzhydroxamate compounds, antioxidants such as propylgallate and copper chelators such a disulfiram. The alternative oxidase is able to oxidise several added polyphenolic substrates and could also oxidise intracellular polyphenolic compounds. It is not yet known if it could directly participate in the metabolism of some xenobiotics. Depending on the stucture of the organic pollutant to be detoxified, the secondary metabolic processes in the plant could also be affected. Many plant specific metabolites, often involved in plant interactions with its environment, have a structure similar to xenobiotics, and detoxification of the latter does probably use, at least partially, the metabolic pathways of the former. For example, most of the natural anthraquinones are glycosylated, whereas glycosyl-transferases are known to be involved in the conjugation of many xenobiotics, probably including sulphonated anthraquinones. It is not yet known if the detoxification mechanisms of sulphonated aromatic compounds are unique and specific to anthraquinone producing plants. Molecules involved in the conjugation of xenobiotics, like glutathione, also play a major role in normal plant metabolism. The presence of xenobiotic compounds can induce the biosynthesis of glutathione transferases and thus an increased use of glutathione. Plant glutathione level and redox status are thus affected under such conditions. On the other hand, phytochelatins are derived from glutathione and involved in the detoxification of trace elements with their –SH groups. In either case, implications on sulphur supply and metabolism are expected. Experimental conditions do also affect plant physiology and biochemistry, and it is not obvious if results obtained with young and small plantlets under well-defined laboratory conditions can be extended to mature plants in the field. However, the large-scale implementation of phytoremediation will be successful only if the “right plant is used at the right place”. Basic physiological and biochemical knowledge is thus required to select the most appropriate plant species, ecotype or cultivar, tolerant to the contaminants to be treated and able to accumulate and detoxify them without impacting its growth and survival.