Pelizaeus-Merzbacher disease (PMD) is an X-linked disorder characterized by dysmyelination of the central nervous system (CNS) caused by mutations involving the proteolipid protein gene (PLP). In addition to point and frameshift mutations in the coding region, duplications involving the entire PLP have been recognized recently as a major genetic abnormality causing PMD. We devised an interphase fluorescence in situ hybridization (FISH) assay to establish an efficient screening test for PLP duplication. Thirteen patients from 11 Japanese PMD families were determined to have PLP duplications. This molecular diagnostic FISH test also readily detected female carriers. Molecular analysis revealed that the size of the duplication and location of the breakpoints showed striking variation. Fiber FISH demonstrated that the duplication is tandem in nature. Haplotype analysis indicated an intrachromosomal origin for the duplication. These results suggest that an unequal sister chromatid exchange in male meiosis is likely to be the major mechanism leading to the formation of the duplication. Patients with the duplication commonly present with a mild PMD phenotype. Two patients with an exceptionally severe clinical phenotype carried large duplications, suggesting that either the larger duplicated segment incorporates additional dosage-sensitive genes or that the location of the duplication junction may affect the phenotype.