Mostly in the liver and the intestinal wall (thus gut health is a priority). But also through the kidneys, lungs, and skin. Toxins are converted into a water soluble form for elimination through the skin bowels, urine, and breath.
There are two phases of detoxification that act as a revolving door for toxins. In phase I, special enzymes breaks down the fat soluble toxins via oxidation. In phase II, the products of phase I are further metabolized into water soluble molecules via conjugation. They are then excreted in bile and urine.
Impairment in phase II conjugation could lead to an accumulation of the toxic intermediates created as a result of phase I. Many factors can influence effective detoxification including age, gender, diet, lifestyle, disease state and intestinal healthy; most notable, however, is biochemical individuality: are we fast or slow metabolizers, i.e., do we have sufficient enzymes to get the job done?