Plasmids are extrachromosomal elements built from a selection of generally quite well understood survival and propagation functions, including replication, partitioning, multimer resolution, post-segregational killing and conjugative transfer. Evolution has favoured clustering of these modules to form plasmid cores or backbones. Co-regulation of these core genes can also provide advantages that favour retention of the backbone organization. Tumour-inducing and symbiosis-determining plasmids appear to co-regulate replication and transfer in response to cell density, both being stimulated at high density. Broad-host-range plasmids of the IncP-1 group, on the other hand, have autogenous control circuits, which allow a burst of expression during establishment in a new host, but a minimum of expression during maintenance. The lessons that plasmids have for clustering and co-regulation may explain the logic and organization of many small bacterial genomes currently being investigated.