A transgenic mouse line, PyLMP.5, exhibited a sex-linked lethality not observed in any other lines expressing the transgene. In this unique line, the transgene integrated into the X chromosome, yielding a simple tandem duplication of the insert sequences with minimal, if any, additional rearrangement of the cellular sequences. The predominant phenotype was a cleft secondary palate and neonatal lethality in males. Survival of females was dependent on the mouse strain background. The disrupted cellular sequences have been mapped to the proximal region of the mouse X chromosome. The disrupted locus may represent the mouse counterpart to a human locus mutated in an X-linked cleft secondary palate syndrome.