The interactions that occur between eukaryotes and bacteria have long been of interest, as knowledge of these processes could lead to the development of novel therapeutics and other potential applications in biotechnology. Many of these interactions are mediated by small molecules, which have subsequently formed the focus of numerous studies. An arsenal of small molecules exhibiting a wide range of activities has been isolated from various sources, including plants, animals and microorganisms. As a number of these compounds are pharmacologically active, there is a strong continued interest in natural product chemistry. Recent developments in this field have focused on two areas: evidence has been gathered to show that secondary metabolites are often produced by symbiotic bacteria, rather than by the eukaryotic host, and the importance of bacterial cell-to-cell signalling in bacteria-host interactions has been confirmed.