The design of advanced, nanostructured materials at the molecular level is of tremendous interest for the scientific and engineering communities because of the broad application of these materials in the biomedical field. Among the available techniques, the layer-by-layer assembly method introduced by Decher and co-workers in 1992 has attracted extensive attention because it possesses extraordinary advantages for biomedical applications: ease of preparation, versatility, capability of incorporating high loadings of different types of biomolecules in the films, fine control over the materials' structure, and robustness of the products under ambient and physiological conditions. In this context, a systematic review of current research on biomedical applications of layer-by-layer assembly is presented. The structure and bioactivity of biomolecules in thin films fabricated by layer-by-layer assembly are introduced. The applications of layer-by-layer assembly in biomimetics, biosensors, drug delivery, protein and cell adhesion, mediation of cellular functions, and implantable materials are addressed. Future developments in the field of biomedical applications of layer-by-layer assembly are also discussed.