The flavenoids or yellowish colouring substances of the flowers are three related compounds kaempferol, quarcetin and myrecetin. They are present mostly as glycosides extractable with alcohol. Dry flowers also yield on chemical analysis a green, amorphous, bitter, toxic substance and a highly pungent essential oil responsible for the characteristic smell.
The bark from the trunk of the tree which is the most favoured medicinally useful part—contains many characterstic biochemicals all named after the Sanskrit name of neem, viz nimba. They are: nimbidin, nimbosterol; margosine—a bitter principle named after the Portuguese name for neem viz margosa and an essential oil (responsible for its smell) and tannin (responsible for the astringent property or the ability to contract tissues and help in healing).
Neem oil contains various acids and the organic sulphur in rich percentage, a very bitter yellowish substance suspected to be an alkaloid, resins, glycosides and fatty acids. The well formed bitter constituents of the plant does not appear to be present as such in the leaves but the precursors of the active principles are predominant there.
Nimbosterol can be obtained from other parts of the plant also. The heart wood or the central core of well grown neem trees is rich with tannin, inorganic calcium potassium and iron salts. In Popular belief the heart wood of some old neem trees is said to resemble the smell of sandal wood.