Mycotoxin analysis in food and biological fluids is receiving more and more concern, in view also of increasing involvement by the European Union regarding legislation. Basically all the analytical steps regarding mycotoxin analysis have to be performed according to accurate criteria which are strictly connected to the quality of results in terms of reliability. The only rationale for reducing this difficulty is to apply quality assurance principles. Quality assurance principles define, in fact, the rules to be observed for performing this analysis with a degree of uncertainty that is as low as may be possible. In particular sampling techniques, if carried out improperly, give rise to uncertainty concerning the representativeness of samples that is so critical as to induce a dramatic source of errors in the final analysis. Therefore it seems appropriate to plan training courses for personnel on the various side-effects related to the available sampling and subsampling techniques depending on the commodity. Other contributions to the overall error derive from improper methodologies used by technicians in the pre-treatment step of the samples (incorrect use of glassware, standard solutions, etc.), and finally from the operations involved in the whole analytical procedure. In addition, the use of reference materials and certified reference materials together with the utilization of validated methods of analysis will be dealt with as concrete procedures for obtaining the certainty of final results of good quality. This aspect takes on a relevant outcome if applied to official control activities from authorized bodies acting at a national level.