Segmental copy-number variations (CNVs) may contribute to genetic variation in humans. In this study, we examined 80 unrelated Japanese individuals using a microarray (2,238 Bac-clones) based comparative genomic hybridization (array-CGH) assay. We found a total of 251 CNVs at 30 different regions in the genome; of these, 14 (termed 'rare' CNVs) were found individually located within distinct genomic regions of 14 individuals, while the remaining 16 CNV regions (termed 'polymorphic' CNVs) were observed in two or more individuals. The rare CNVs were confirmed by quantitative polymerase chain reactions, and characterized more precisely than in previous reports using array CGH. Distinctive features of these CNVs were observed: most prominent was that the majority of the rare CNVs presented on Bac-clones that did not overlap with regions of segmental duplication. About 90% of the polymorphic CNVs observed in this population had been previously identified, with the majority of those polymorphic CNVs located in regions of segmental duplication. It is likely, therefore, that rare and polymorphic CNVs arise through different genetic mechanisms. Since more than half of the rare CNVs are novel, it is also likely that different human populations bear different CNVs, as is the case for single-nucleotide-polymorphisms (SNPs) and insertion-deletion (indel) polymorphisms.