The dissection of chromosomes followed by extraction of specific DNA fragments constitutes a topic of high interest, especially for cytogenetic studies in the post genome era. The dissected chromosomes can be used in various conventional applications, including establishing probes for fluorescence in situ hybridization (FISH), the generation of chromosome band-specific libraries and physical mapping for cytogenetic analysis. For this purpose, several reports using micro-and nano-dissection methods by micro-manipulators have been published. In the present study, we developed a functional chromosome dissection chip that can dissect various chromosomes in one-chip by using the pattern chip with nanometer-scale porous anodic alumina. The porous anodic alumina that is to make use of self-organized nano-array materials as a template for the pattern chip has a highly oriented porous structure with very uniform and nearly parallel pores that can be organized in an almost precise close-packed hexagonal structure. The most characteristic feature of this material has been emphasized with the extremely high aspect ratio of their channels that is difficult to achieve with conventional lithographic techniques. We have proceeded as follows for this study; the pattern chip with nanometer-scale porous anodic alumina was fabricated. Then, metaphase chromosomes were prepared by dropping the cell suspension onto pattern chip and air-drying until use. Finally, the chromosomes that were penetrated into the nano-pores on the pattern chip by pressing with a tender silicon plate were dissected with nanometer size. This technique will form the basis for the development of new system such as "Nano-scale chromosome dissection chip" that arrays chromosomal fragments with nanometer scale on a chip for DNA and protein nano-analysis. (c) 2005 Elsevier B.V. All rights reserved.