Background: Public health genomics is a new field that brings the findings of research in genetic and molecular technologies together with public health. The purpose of this paper is to examine the interface between this new emerging field and that of public health intelligence. We describe the possible areas of integration between genomics and public health, suggesting a future potential role for the Public Health Observatories. Methods: A small group comprising of a public health geneticist and representatives from Public Health Observatories met and discussed the ways in which the public health information and intelligence community might contribute to the developing agenda of public health genomics. Results: The results of the deliberations are presented in this paper, and a combination of short, medium and longer term possibilities are described. Also, necessary changes and additions to routinely collected data are proposed. Conclusions: The emerging field of public health genomics has implications for the collection, management and analysis of routine data. The benefits of this will accrue over time, but changes need to be made now in order to make the best use of these developments. A possible supporting action plan for the development of public health genomics within Public Health Observatories is proposed.