Ciliates, microbial eukaryotes, have been important experimental organisms for >100 years, contributing to the discovery and understanding of self-splicing RNA, telomere biochemistry and transcriptional regulation by histone modification. We have completed a pilot sequencing project of the Oxytricha trifallax macronuclear (MAC) genome. When complete, this genome sequence, along with the emerging Tetrahymena thermophila and Paramecium tetraurelia sequences, will provide an important resource for basic eukaryotic cell biology, molecular evolution and the related apicomplexan parasites, such as Plasmodium spp.