The zeste gene of Drosophila regulates the expression of certain other genes like white, bithorax and decapentaplegic in a manner dependent on chromosome pairing. The genetic evidence suggests that its product interacts with the genes at the level of transcription. We have cloned the zeste region from fragments microdissected from the 3A1-4 region of the X chromosome and mapped the breakpoints of several rearrangements which localise the gene. We have isolated dysgenic zeste mutants which contain P element sequences inserted in the same region. DNA rearrangements were found in some zeste mutants but were not detected in the z1, z0p6 or z0p11 mutants. The changes are localised to a Bam 4.0-kb fragment from which originates a 2.4-kb RNA species. This transcript is altered in some zeste mutants but is not visibly affected in Z1 or z0p6 mutants. The region bears no homology to the white gene or its vicinity but cross-hybridises to many other genomic sequences in Drosophila.