In C. elegans and D. melanogaster, specialized sites have an important role in meiotic recombination. Recent evidence has shown that these sites in C. elegans have a role in synapsis. Here we compare the initiation of synapsis in organisms with specialized sites and those without. We propose that, early in prophase, synapsis requires an initiator to overcome inhibitory factors that function to prevent synaptonemal complex (SC) formation between nonhomologous sequences. These initiators of SC formation can be stimulated by crossover sites, (...) possibly other types of recombination sites and also specialized sites where recombination does not occur. BioEssays 29: 217–226, 2007. © 2007 Wiley Periodicals, Inc. (shrink)