Scientists and bioengineers have dreamed of designing materials from the bottom up with the finest detail and ultimate control at the single molecular level. The discovery of a class of self-assembling peptides that spontaneously undergo self-organization into well-ordered structures opened a new avenue for molecular fabrication of biological materials. Since this discovery, diverse classes of short peptides have been invented with broad applications, including 3D tissue cell culture, reparative and regenerative medicine, tissue engineering, slow drug release and medical device development. Molecular design of new materials using short peptides is poised to become increasingly important in biomedical research, biomedical technology and medicine, and is covered in this tutorial review.