Chemistry has always characterized in the emphasis on the qualitative properties and in its opposition to reductionist philosophy. In this book, I show the importance of structured matter at the molecular level as source of the wealth of reality. This creates a number of different entities as particular as to deserve a specific name. As a consequence, the reductionist perspective is insufficient to make us understand one of the most important aspects of the real world: the existence of ordered entities, each one with its own structure and its organization. The idea of this book is that the reductionist and holistic approaches are partial: they capture important aspects of reality, and neglect others that are equally important. Both are essential for a scientific description of the world but only just taken together give a balanced description of reality. Today, the irreducibility of real entities to the reductionist approach, have bought new aspects in Systemic and in the so-called “Sciences of Complexity”. This book can be linked to these important cultural areas.