Ciguatera Poisoning (CP) has been considered an emerging risk in European subtropical areas of the Atlantic Coast of Europe. The characterization of this emerging risk prompted the interest of the European Health Authorities. This characterization has been carried out over the last eight years under the support of EFSA. The lack of reference materials commercially available has been the main challenge for the method development required for the characterization of the ciguatoxins involved in the contamination. An intensive and challenging work, in the absence of standards commercially available, has been carried out, not only in the optimization of sample pretreatment protocols, but also in the development of analytical methods for screening/quantitation and confirmation. The combination of toxicological assays, such as N2a-MTT cell assay with chemical methods by liquid chromatography coupled to mass Spectrometry (LC-MS) has resulted on a very efficient tool that allowed the characterization of Caribbean ciguatoxins as the responsible of the CP in the areas of study. The analytical tools developed also allowed the preparation of ciguatoxins reference material for laboratory use. The main achievements and challenges on this risk characterization from the analytical chemistry point of view is going to be presented and discussed.