Methyl 4-Aminothiophene-3-carboxylate Hydrochloride is used as a reagent in the synthesis of benzisothiazolylpiperazinylbutyl heterocyclic carboxamide antipsychotics. Methyl 4-Aminothiophene-3-carboxylate Hydrochloride is also used as the starting material in the synthesis of 1H-Thieno[3,4-d]pyrimidine-2,4-dione (T344325) which is an analog of thieno[3,4-d]pyrimidine and can serve as a fluorescent probe sensing mismatched pairs.