Incontinentia pigmenti (IP) is a rare disorder which affects organs and tissues of ectodermal and mesodermal origin. It is characterized by swirled patterns of hyperpigmentation. In some cases, the condition is also associated with malformations of the teeth, nails, skeleton, hair, eyes, and the central nervous system. The disorder is inherited as an X-linked dominant trait and mostly affects females. However, there have been several cases of IP in males that survived to birth. While IP in females could be caused by a skewed pattern of X-inactivation, three mechanisms: namely, the half-chromatid hypothesis, unstable premutation, and a higher rate of de-novo germline mutations, have been proposed to explain the survival of affected male patients. Cytogenetic studies in several sporadic cases with signs similar to IP exhibited an X/autosomal translocation involving a breakpoint at Xp11, suggesting a gene locus on Xp11 (IP1). Linkage analysis of familial IP, on the other hand, has identified a second locus, in the Xq28 region (IP2). Molecular genetic analysis of two candidate genes located at Xp11 and Xq28, as well as the human homologue of the murine Str gene, failed to reveal any disease-causing mutations. Although heterozygous female mice deficient for the IKKγ / NEMO gene exhibited dermatopathy similar to that in human IP, studies of the gene in human IP have not yet been available. In an effort to isolate the genes causing IP, cosmid clones containing the translocation breakpoint located at Xp11 and the transcriptional map of the Xq28 region were constructed. These maps could be invaluable tools in the identification of genes in the near future.