The chemical reaction of lipid peroxidation consists of three phases: initiation, propagation, and termination.
In the initiation phase, a pro-oxidant hydroxyl radical () abstracts the hydrogen at the allylic position (–CH–CH=CH) or methine bridge (=CH−) on the stable lipid substrate, typically a polyunsaturated fatty acid (PUFA), to form the lipid radical () and water (HO).
In the propagation phase, the lipid radical () reacts with molecular oxygen () to form a lipid hydroperoxyl radical (). The lipid hydroperoxyl radical () can further abstract hydrogen from a new PUFA substrate, forming another lipid radical () and now finally a lipid hydroperoxide (LOOH). 
The lipid hydroperoxyl radical () can also undergo a variety of reactions to produce new radicals.
The additional lipid radical () continues the chain reaction, whilst the lipid hydroperoxide (LOOH) is the primary end product. The formation of lipid radicals is sensitive to the kinetic isotope effect. Reinforced lipids in the membrane can suppress the chain reaction of lipid peroxidation.
The termination step can vary, in both its actual chemical reaction and when it will occur. Lipid peroxidation is a self-propagating chain reaction and will proceed until the lipid substrate is consumed and the last two remaining radicals combine, or a reaction which terminates it occurs. Termination can occur when two lipid hydroperoxyl radicals () react to form peroxide and oxygen (O). Termination can also occur when the concentration of radical species is high.
The primary products of lipid peroxidation are lipid hydroperoxides (LOOH).