Microphthalmia with linear skin defects (MLS) syndrome is an X-linked disorder presenting only in XX individuals. It is characterised by dysmorphic features such as microphthalmia, sclerocornea, and linear streaks of erythematous and hypoplastic skin restricted to the head and neck. Karyotype analyses have so far revealed a terminal deletion or translocation causing monosomy for the distal Xp region (Xp22.3) in all patients. We have used existing cosmid clones from the region to perform a saturation screen for AC-type microsatellites with the goal of facilitating analysis of five novel patients with features of MLS. Three of these cases had an Xp22.3 abnormality, while the other two showed some characteristic features of MLS but had apparently normal karyotypes. Forty-two novel microsatellite markers have now been developed from the 1.7 Mb cloned interval. Ninety-three percent of the novel markers exhibited allelic variation, representing an average of one polymorphic PCR-based marker (STR) every 41 kb.