The International Conference on Self-Assembly in Confined Spaces (SACS16), organized by the laboratory of Bionanoplasmonics at CIC biomaGUNE, took place between the 25th and 27th of October 2016 at the Miramar Royal Palace of San Sebastián. The meeting brought together some of the most active and recognized chemists, physicists, theoreticians, engineers, and biomedical researchers to discuss the use of self-assembly as a tool to design, organize and provide special functions to nanomaterials. The program covered the fields of molecular and nanoparticle Self-Assembly, interfacial properties, biomedical applications of self-assembled systems and advanced characterization techniques. The conference was attended by more than 120 researchers. During three days, 16 prominent scientists delivered plenary talks and selected researchers provided 18 contributed talks and 75 poster presentations.