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N,O-Dimethylhydroxylamine hydrochloride is not typically used as a pharmaceutical drug substance or API on its own, but it can be used as an intermediate in the synthesis of various pharmaceutical compounds. It is commonly used as a reducing agent in organic synthesis, particularly in the synthesis of nitroso compounds.

In the pharmaceutical industry, N,O-Dimethylhydroxylamine hydrochloride can be used in the synthesis of several drug molecules such as ranolazine and zolmitriptan. It is also used in the synthesis of certain agrochemicals, rubber chemicals, and dyes.