The concept of molecular nanomachines has become a reality in the past few years in organic and supramolecular chemistry, in biochemistry and in atom-scale manipulation with the scanning tunnelling microscope (STM).

In chemistry, molecules can be designed and synthesized to have specific electrical, mechanical, optical or reactive properties. In biochemistry, single natural biomolecules can be isolated and activated as nanomachines. In atom-scale manipulation, the STM can be used to power and to control the operation of individual molecules as molecular nanomachines.

The fields of chemical synthesis, biomolecular machines and atom-scale manipulations, have each developed as a separate entity. However, mutual integration of these different research fields appears to be a very fruitful approach for the future of molecular nanomachines. This special section of Journal of Physics: Condensed Matter is the follow-up to a meeting held in Les Houches (France) on 17–21 January 2005 on molecular nanomachines. The section aims to contribute to the readers' understanding by giving a clear overview of the principal issues of molecular nanomachines. We hope that it will facilitate new collaborations between researchers from these different fields, so necessary for the integrated development of molecular nanomachines.