The chiral pair alkannin and shikonin (A/S) and their isohexenylnaphthazarin (IHN) esters, which are naturally occurring hydroxynaphthoquinones (HNQ), are potent pharmaceutical substances with a wide spectrum of biological activity. The stability of A/S and their derivatives during process and storage is crucial to their use as drugs, cosmetics and food additives. The influence of alkaline media and of IHN esters hydrolysis was experimentally investigated on IHN polymerization by size exclusion chromatography (SEC). It was proved that during IHN esters hydrolysis, polymeric A/S and IHN are formed. An optimization of the hydrolysis conditions of IHN esters was also approached in terms of polymerization. Hydrolysis of IHN from a pure mixture of pigments proved preferable to that of preliminary root extracts by means of IHN polymerization, even for analytical determination; non-polar solvents are proposed for the extraction of IHN from roots, followed by hydrolysis, aiming to minimize the polymeric IHN and A/S formed. It was also proved that polymerization of IHN in alkaline media and during hydrolysis of IHN esters proceeds through the intermediate formation of semiquinones; after acidification, coupling of semiquinones with phenoxyl radicals results in polymeric IHN structures.