Bacterial secretion systems play essential roles in pathogenesis and also in maintaining lines of communication between bacterial cells in the bacterial microflora or between commensal bacteria and their host. Recent breakthroughs in the field have yielded some novel insights into the mechanisms by which these systems operate. This issue of Philosophical Transactions B seeks to provide a detailed survey of the field, with an emphasis on mechanisms and how their unravelling might provide a new future for antibiotics research.