It serves as a building block for synthesizing potential drug molecules especially those containing nitrogen heterocycles. It is used in reactions involving condensation and cyclization due to its functional group reactivity. It may be used in studies involving enzyme interactions or molecular modeling because of its structural similarity to biologically relevant amidines.

The primary purpose of acetamidine hydrochloride is as a chemical intermediate. It is used in organic synthesis for the preparation of more complex nitrogen-containing compounds.

Acetamidine itself contains an amidine functional group which is characterized by a carbon atom double-bonded to a nitrogen atom and single-bonded to another nitrogen. In its hydrochloride form the compound exists as a protonated salt making it more stable and easier to store. It is generally used in controlled chemical environments rather than in everyday commercial products.