Science presents us with a variety of accounts of the world. While some of these accounts posit deep theoretical structure and fundamental entities, others do not. But which of these approaches is the right one? How should science conceptualize the world? And what is the relation between the various accounts? Opinions on these issues diverge wildly in philosophy of science. At one extreme are reductionists who argue that higher-level theories should, in principle, be incorporated in, or eliminated by, the basic-level theory. According to this view, higher-level theories do not ultimately exhibit conceptual integrity or provide genuine explanations. At the other extreme are pluralists who take higher levels of description and explanation seriously and argue for their independence and indispensability. It was the aim of the first Sydney–Tilburg conference on “Reduction and the Special Sciences”, which took place at the Tilburg Center for Logic and Philosophy of Science (TiLPS) in Tilburg, The Netherlands, over the 10–12th April 2008, to bring researchers working on these questions together and provide a platform to discuss them in a focused way. The papers in this special issue were presented at this conference. We would like to thank the Royal Netherlands Academy of Art and Sciences (KNAW), the Sydney Centre for the Foundations of Science at the University of Sydney and TiLPS for financial and institutional support. We also thank the authors and referees of the papers for their work, and Hans Rott for his support of this project.