In Europe (and worldwide), we currently largely rely on conventional agricultural systems, in which synthetic pesticides and other agrochemical products are allowed and applied. The discussion on pesticide residues must be situated in this context. Organic production does not allow the use of synthetic pesticides, artificial fertilizers or any herbicides. However, their widespread use by the majority of farmers creates an omnipresent risk of contamination in the whole food supply chain. This is especially the case for crops, as the pollutants which can be easily detected from the technical point of view, such as pesticides, are well known to travel by air, ground water or being transferred by handling in the food chain or are persistent in the soil for a long time. Food production is operating in an open system, after all. Furthermore, the huge progress in terms of analytical processes and methods make the detection of residues and contaminants even more frequent than in the past. The organic movement does not underestimate the issue of residues of pesticides and the risk that non-allowed substances are used. Therefore, it is important that investigations take place to clarify if the reason of a presence is a violation of or a non-compliance with the requirements of the organic regulations. A process-based approach is the key for organic control systems here, in which taking samples and having laboratory analysis are one of the tools.