In eukaryotes, ribosome synthesis largely takes place in a specialized nuclear domain - the nucleolus. It has recently become apparent that this organelle is involved in the biogenesis of most cellular ribonucleoprotein particles (RNPs), as well as in cell-cycle regulation, making it central to gene expression. The field has traditionally acknowledged that each nucleolus is organized in three morphologically distinct compartments. Here, however, we discuss our view that in fact many eukaryotes have bipartite nucleoli. We propose that, during evolution, a third nucleolar compartment emerged at the transition between the anamniotes and the amniotes, following a substantial increase in size of the rDNA intergenic region. We believe that these conclusions have important implications for understanding the structure-function relationships within this key cellular organelle.