The production and distribution of counterfeit drugs is a serious worldwide health problem. One recent example is the appearance of fake artesunate antimalarial tablets in Southeast Asia. Due to the malevolent circumstances in which these fakes are produced, concern over the presence of toxic tablet ingredients is very much a legitimate health issue. Therefore, quantification of the amount of active ingredient present in tablets marketed as artesunate, a drug used for the treatment of the multidrug-resistant Plasmodium falciparum malaria in Southeast Asia required liquid chromatography coupled to mass spectrometry (LC-MS). This quantification allows the classification of the tablets as genuine, sub-therapeutic or fake and the validation of field results using colorimetric tests. During the LC-MS experiments, there were the observations that several of the samples contained a “wrong” active ingredient (AI). This was identified via accurate mass measurements, chromatographic retention time and in-source collision-induced dissociation (CID)as erythromycin, a common antibiotic. Using multivariate unsupervised clustering algorithms, the LC-MS data was utilized for “chemically fingerprinting” the fake tablet samples and investigating the similarities between them. The results of this initial survey show a correlation between sample origin, the different types of fake authentication holograms found in the packaging and sample composition.