The macronuclear genomes of spirotrichous ciliates are almost entirely polyploid, single-gene chromosomes ("nanochromosomes"). We recently performed a pilot genome project for a member of this group, Oxytricha trifallax ( Sterkiella histriomuscorum), in which approximately 2000 nanochromosomes were cloned at random and end-sequenced. Here we describe the global properties of the coding regions predicted for these molecules, including nucleotide composition, codon usage, and intron properties. In identifying splice donor, acceptor and branch sites, we found that longer introns in Oxytricha have a stronger signal at the donor site than do smaller introns, as has been found for Caenorhabditis elegans and Drosophila, despite the overall small size of the introns. A systematic search for multi-gene chromosomes identified 11 candidate nanochromosomes. We compare the results from this large dataset with those obtained from earlier studies and with statistics recorded from ciliates and other eukaryotes.