We analyzed the extent, reproducibility, and developmental control of genomic rearrangements in the somatic macronucleus of the ciliate Tetrahymena thermophila. To exclude differences caused by genetic polymorphisms, we constructed whole-genome homozygotes, and we compared the homozygous progeny derived from single macronuclear differentiation events. This strategy enabled us to identify a novel form of variable rearrangement and to confirm previous findings that rearranged sequences occur at a high frequency in the Tetrahymena genome. Rearrangements studied here were deletions of both unique and interchromosomally dispersed repetitive DNA sequences involving DNA rejoining of internal, nontelomeric regions of macronuclear DNAs. We showed that although rearrangements of some sequence classes are reproducible among independently developed macronuclei, other specific sequence classes are variably rearranged in macronuclear development. The variable somatic genomes so produced may be the source of phenotypically variant cell lines.A long-standing question in eucaryote development is the extent and nature of DNA rearrangement during development. Irreversible differential gene alterations have been found in a number of widely separated systems. Developmentally programmed examples of these include the chromosomal diminution found in nematodes (reviewed in reference 36), some insects and crustaceans (reviewed in references 5 and 35), and ciliates (reviewed in references 15, 24, and 25) and DNA rearrangements which occur in antibody-producing lymohocytes (reviewed in reference 34).The ciliated protozoan Tetrahymena thermophila affords an excellent model system to determine the extent, nature, and developmental timing of rearrangements during development of the somatic nucleus. T. thermophila is a unicellular organism containing two nuclei, a transcriptionally inactive germline nucleus (micronucleus) and a somatic, amitotically dividing macronucleus which is the site of gene expression. In the sexual process, conjugation, haploid micronuclei generated by meiosis are exchanged between the paired cells and subsequently fused. A division product of the newly diploid micronucleus in each cell differentiates into a new macronucleus, replacing the old macronucleus, which is destroyed (for reviews, see references 12, 14, and 15). Since these cells subsequenly divide vegetatively by binary fission in the absence of conjugation (which requires specific culture conditions as well as interaction between two cells of different mating types), large clonal populations can be obtained at given stages of development, and pure preparations can be made of macronuclei and their parent micronuclei.