by Dominic C. Chow 1,3 , Matthew S. Johannes 2,3 , Woo-Kyung Lee 2,3 , Robert L. Clark 2,3 , Stefan Zauscher 2,3 , and Ashutosh Chilkoti 1,3* 1 Department of Biomedical Engineering, 2 Department of Mechanical Engineering and Materials Science, 3 Center for Biologically Inspired Materials and Material Systems, Duke University, Durham, North Carolina 27708-0281, USA *E-mail: chilkoti@duke.edu The advances in biotechnology and nanotechnology are spawning a new and exciting manufacturing tool – bionanofabrication – which enables revolutionary ways of building complex bionanostructures on surfaces with nanometer precision. Here, we highlight the opportunities and challenges in the development of this emerging technology and discuss its use in genomics, proteomics, nanostructures, nanomaterials, drug discovery, and synthetic biology. To provide useful insights into the future directions of bionanofabrication, current developments in characterization techniques, fabrication methods, and their integration and control in manufacturing processes are discussed. The excitement generated by nanotechnology derives from the promise of manipulating matter atom-by-atom and molecule-by-molecule to create devices with performances and functionalites that are orders-of-magnitude better than those provided by current manufacturing technologies. The rapid development of nanoscale patterning and lithography technologies plays a substantial role in realizing this dream. The invention of synthetic photosensitive compounds, e.g. poly(vinyl cinnamate)- based negative photoresists 1 and diazoquinone-based positive photoresist 2 , in the 1930s laid the foundation for many modern-day lithography and etching techniques used in microfabrication. For years, devices such as microprocessors 3 and microelectromechanical systems (MEMS) 4,5 have been machined out of crystalline Si by lithography (e.g. photolithography, X-ray lithography, and electron- and ion-beam lithography), as well as by bulk micromachining processes such as wet and dry chemical etching, SiO 2 growth, and vapor deposition 6 . While engineers and scientists race to shrink the size of transistors and MEMS components through nanofabrication to create the next generation of high-performance electronic devices, biologists and life scientists have just begun to employ micropatterning and, to a more limited extent, nanopatterning techniques to build high-throughput detection systems for genomic and proteomic studies 7-9 . with biomolecules ISSN:1369 7021 © Elsevier Ltd 2005 Nanofabrication December 2005 30