This EMBO Conference focuses on comparative genomics of eukaryotic microorganisms, including the Excavates and Archaeoplastids, Amoebozoa and Choanozoa, as well as the better studied Chromalveolates and Fungi. There are platforms for comparative genomics of prokaryotes and of higher eukaryotes but no forum concentrating on eukaryotic microbes. We now have genome sequences from most of the major branches of eukaryotes and should be able to address fundamental questions such as the origins of multicellularity. This wealth of genomic information offers several unique opportunities that will be discussed at the conference including the various evolutionary lineages of eukaryotic microorganisms, as well as the origin of multicellularity, sex, and regulatory and metabolic networks.