Hexamethyldisilazane is employed as a reagent in many organic reactions: 
1) HMDS is used as a reagent in condensation reactions of heterocyclic compounds such as in the microwave synthesis of a derivative of xanthine:
2) The HMDS mediated trimethylsilylation of alcohols, thiols, amines and amino acids as protective groups or for intermediary organosilicon compounds is found to be very efficient and replaced TMSCl reagent. 
Silylation of glutamic acid with excess hexamethyldisilazane and catalytic TMSCl in either refluxing xylene or acetonitrile followed by dilution with alcohol (methanol or ethanol) yields the derived lactam pyroglutamic acid in good yield.
HMDS in the presence of catalytic iodine facilitates the silylation of alcohols in excellent yields.
3) HMDS can be used to silylate laboratory glassware and make it hydrophobic, or automobile glass, just as Rain-X does.
4) In gas chromatography, HMDS can be used to silylate OH groups of organic compounds to increase volatility, this way enabling GC-analysis of chemicals that are otherwise non-volatile.