In the past perchlorates were quite widely used in the synthesis of coordination compounds because their larger size (compared to halides) and excellent hydrogen bonding abilities made them highly effective counter-ions for complexes with ammine, aquo and halido ligands, often yielding highly crystalline products.

However because of the hazards (see Safety Section below) associated with their use they have been largely superseded in most labs by much less risky counterions like fluoroborate (BF4–, PF6– and related anions.

[6] It is used for denaturating proteins in biochemistry and in standard DNA extraction and hybridization reactions in molecular biology.

When mixed with organic compounds extreme combustion reactions can result, hence the use of such materials in fireworks, low tech rocket propellants and improvised explosives.

Significant concerns have been raised about the environmental impacts of perchlorates because of its ability to disrupt iodide uptake and metabolism.