Microfabrication traditionally has been limited to silicon as demonstrated by the multi-billion dollar industry. The field is now understandably developing into a combination of physics, chemistry and biology in very non-traditional approaches to develop functional devices.Some examples are on-chip hybridization of deoxyribonucleic acid (DNA) and optical detection, DNA/protein/cell detection at the micro scale for diagnostics in medical, military, and food safety applications, etc. One area where silicon based nanotechnology can have an immediate and far reaching impact is sensing biological molecules and their processes, especially in genomics and proteomics. The promise of nanofabrication lies in the special ability to fabricate devices not only down to the scales of bacteria and viruses, but even down to the scales of the smallest biological entities, such as DNA! Nanotechnology and BioMEMS will have a significant impact on medicine and biology in the areas of single cell detection, diagnosis and combating disease, providing specificity of drug delivery for therapy, and avoiding time consuming steps to provide faster results and solutions to the patient. Integration of biology and silicon at the micro and nano scale offers tremendous opportunities for solving important problems in biology and medicine and enables a wide range of applications in diagnostics, therapeutics, and tissue engineering. This paper reviews state of the art in silicon-based bioMEMS and bionanotechnology as well as the future challenges and opportunities. A range of silicon devices integrating microsystems engineering with biology are discussed with focus on rapid detection of biological entities and development of point of care devices using electrical or mechanical phenomena at the micro and nano scale.