Of the various radicals involved in autoxidation, the peroxy radical is much more stable than the other alkoxy, hydroxy or alkyl radicals. It is thus quite able to select a hydrogen atom from an allylic group (DR-H=322 kJ/mole) or even from a bi-allylic position as in linoleic or linolenic moieties (DR-H=272 kJ/mole) instead of the much more inaccessible alkyl radical which show dissociation energies above the 400 kJ/mole mark.

That these energy differences matter is shown by the difference in reaction rates and induction periods observed at moderate temperatures when linolenic (two bi-allylic positions) or linoleic (one bi-allylic position) are suffering autoxidation, relative to that shown by oleic (one allylic position) or even to the stability of stearic moieties.

The peroxy radical formed during propagation is slow reacting and therefore it selectively abstracts the most weakly bound H-atom from a fat molecule. It differs in this property from, for example, the substantiallly more reactive hydroxy (HO^· ) and alkoxy (RO^· ) radicals.

As may be seen from the schematic depictions, an oleic substrate will actually yield as result of the first autoxidation stage a mixture of 8-, 9-, 10-, and 11- hydroperoxides. If both geometrical (cis-trans) and stereochemical (R-S) isomerism is taken into acount - as of course it should be - this means that sixteen different hydroperoxides are produced. Inspection of the diagram shows that it is after abstraction of one hydrogen atom that the bond between positions 9 and 10 loses its character as a double bond, hence becoming prone to rotational isomerisation to a cis geometry, thermodinamically more stable. When the double bond migrates, the general case is that the trans isomer be predominant, say twice as abundant as the cis .

The methylene group in position 11 is the initial site for the abstraction of an H-atom in oxidation of linoleic acid, because it is the only bi-allylic position. The pentadienyl radical generated will after reaction with oxygen yield a conjugated hydroperoxidiene system with oxygen at positions 8 or 13 and migration of the double bond nearest to it, rather than that which would result from substitution at the original position 11 or those in which this position remains an unchanged methylene group. Geometric isomerism might or might not occur with double bond migration, and a number of isomers will therefore result.

The hydroperoxides have a UV maximum absorption at 235 nm and can be resolved by high performance liquid chromatography of their methyl esters, either directly or after reduction to hydroxydienes.

Nevertheless, the monoallylic groups in linoleic acid (positions 8 and 14 in the molecule), in addition to the bi-allylic group (position 11), also react as allylic systems to a small extent, yielding hydroperoxides (8-, 10-, 12- and 14-OOH), each of them a mixture of cis and trans isomers with two isolated double bonds. These minor monohydroperoxides only amount to ca. 4% in total.

The hydroperoxides resulting from autoxidation (³O₂) and photoxidation (¹O₂) of unsaturated fatty acids are shown in table form

In an entirely similar way, it can be seen that autoxidation of linolenic acid yields four monohydroperoxides (stereochemical and geometric isomerism not included). Formation of the monohydroperoxides is easily achieved by H-abstraction from the bi-allylic positions 11 and 14. Each of the resulting pentadiene radicals will then suffer addition of oxygen and of a hydrogen atom as shown for linoleic acid. However, the positional isomers are not formed in equimolar amounts; a clear predominance of the 9- and 16- isomers is apparent in the table above. The configuration of the conjugated double bonds again depends on reaction conditions. Cis-hydroperoxides are the main products if the reaction is performed at temperatures below 40ºC.

Reactions involving b-fragmentation and cyclisation may compete with hydrogen abstraction by peroxy radical, thus keeping the conversion to hydroperoxide from being fully effective. Moreover, both allyl peroxy radicals and hydroperoxides can undergo 1-3 rearrangement via a b-fragmentation mechanism, and after a new bond to oxygen is made, in a positional isomer of the starting material, in a process which is akin to internal return.