The perception of markets delivering a Pareto optimal solution with distribution of benefits and value creation along the supply chain has been evolving from a theoretical perspective and respective assumptions toward more pragmatic and sophisticated analysis. Food and agricultural production, at farm level, frequently faces great challenges and deviations from theory optimal solutions, mainly when markets do not have the necessary conditions for “perfect functioning”. Institutional innovation and regulations from the supply side and from the demand side have been able to offer solutions, some of them science based. Those examples deserve attention and can offer sound base for improvements in our knowledge about market behaviour and development for improved dynamics and innovation in the food systems. The analysis will be centred in case studies in Europe, Africa and Latin America, providing examples where science has been playing an important role for good market performances. In the wine sector in Europe, regulations started very early, and were based on market needs and value creation strategies. Food aid for development purposes also evolved during the last decades, from tangible goods distribution toward other forms of cooperation for development, which has been very important for African countries. Last but not least, we would like to address the examples of private sector organizations with market regulatory interventions, such as the sugar cane sector with a scientific based support from research team’s efforts (like CEPEA at the University of S. Paulo/Brazil, among others).