Saint John’s wort (H. perforatum L., SJW) products are widely used in different forms and regulated by different legislations. Previous studies highlighted the significant variability in the quality of marketed products of different provenance [1], [2]. In addition to extremely low concentrations of hypericins and the detection of dyes, a number of samples were found to showcase chemical fingerprints distinct from the pharmacopoeial description. This project aims to establish baseline standards for high quality materia prima including an understanding of the natural variability. Therefore, a collection of raw materials from 14 countries was analysed using NMR-based metabolomics profiling and HPTLC. A number of samples’ heavy metal content was determined. The analysis of the raw materials showed some degree of variability, which is non-significant compared to the marketed products’ variation. The chemical differences noticed where identified, disambiguated and preliminarily assigned to 3 fingerprint types. The existence of four geographically distinct subspecies of SJW [3] was investigated as a potential factor behind these differences and an attempt to build a statistical model to predict the provenance of the samples based on NMR results was made. The difference between the legal limits for cadmium prescribed by the European Pharmacopoeia and WHO, respectively, highlights the need for regulatory concordance. Understanding the materia prima remains a challenge due to the numerous factors involved. Therefore, regulatory agencies need to consider and assess this complexity, in order to resolve quality challenges in the first step of the value chain.