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Tylenol overdose is an extreme example of what can happen if things do not work properly but there are other extreme examples and many more where the consequences may not be death, but impaired functioning and less than optimum health. There are two main pathways involved in the detoxification process. They take place in the liver. In general it involves altering chemical structures of substances so that they can be excreted in the bile, urine, sweat and feces and not build up and get stored in tissues in the body. For some substances they are temporarily more toxic after step one and if step two does not happen or happens too slowly they are more toxic then when ingested. The process sounds is very complicated and requires many enzymes and cofactors for these enzymes. It also requires all the building blocks to be able to manufacture glutathione. The ability to add sulfur groups and methyl groups is crucial during this process and any deficit will leave the pathways working at less than optimum efficiency. This means there are many B vitamins as well as amino acids that can act as sulfur and methyl donors that are necessary for this process to work.
Because of the complexity of this system it means there are multiple different ways in which it can malfunction. There can be congenital deficits in these pathways, liver disease (infectious, inflammatory, malignancy) that can have a negative impact. Poor nutrition (either from poor intake or inability to absorb due to gut inflammation), toxic exposures, as well as epigentic changes can all play a role in the efficiency of the detoxification pathways.
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