Despite its prominence in scientific research, molecular medicine has not received sufficient attention by the philosophical community. Philosophy of Molecular Medicine: Foundational Issues in Theory and Practice aims at a systematic investigation of a number of foundational issues in the field of molecular medicine. The volume is organized around four broad modules focusing, respectively, on the following key aspects: What are the nature, scope and limits of molecular medicine? How does it provide explanations? How does it represent and model phenomena of interest? How does it infer new knowledge from data and experiments? The essays collected here, authored by prominent scientists and philosophers of science, focus on a handful of mainstream topics in the philosophical literature, such as causation, explanation, modeling, and scientific inference. These previously unpublished contributions shed new light on these traditional topics by integrating them with problems, methods, and results from three prominent areas of contemporary biomedical science: basic research, translational and clinical research, and clinical practice.