Mycotoxin contamination of food and feedstuffs is among the top priority issues regarding human and animal safety. On one hand , the consumers are increasingly concerned by public health-related issues and show high preoccupation about the risks associated with human exposure to mycotoxins. This latter can produce both acute and chronic toxic effects ranging from death to deleterious effects on the immunity system, hepatic and kidney functions, central nervous and the alimentary tract.. On the other hand, the mycotoxins attract worldwide attention because of the significant economic losses associated with their impact on human health, animal productivity and both domestic and international trades. Limits of these substances in traded goods are becoming more and more restrictive to the point of turning into one of the main potential barriers for Southern agricultural products to access international markets. Those mycotoxins that are currently considered to be of worldwide importance include the aflatoxins, the trichothecenes, zearalenone, the fumonisins and ochratoxin A. Mold and mycotoxin contamination may occur in any point of the supply chain, both in production and post harvest stages.. The main interventions that may be employed for the control of mycotoxins are prevention of contamination, identification and segregation of contaminated material, and detoxification. Alternatively a modification of a food processing operation can also help to control the level of mycotoxins in foods. This paper presents the whole framework of a EU funded project that addresses the methodological and analytical issues associated with the establishment of a Food Quality Management System (FQMS), for controlling mycotoxins in cereal chains, in Latin America South Cone countries. Alternative fast analytical techniques are tested for subsequent use on field. All critical points in cereal chains are identified, from farm to market and solutions are proposed and validated, according to