The invention concerns a method for analyzing a sample of a complex molecule relatively to a reference batch of the same complex molecule. Said method is characterized in that it consists in breaking up the complex molecule into at least two molecular sub-entities; in determining, on the basis of the atomic sites of said products of the breakup involved in the breakup reactions, the isotope(s) to be analyzed; and in establishing, for at least part of the breakup products, their isotopic profile; and in comparing the isotopic profile of the products of the breakup with the isotopic profile of the raw material(s) previously indexed and/or with the isotopic profile of the reference complex molecule subjected to the same breakup reactions. The invention is useful for detecting counterfeiting in manufacturing processes.