The most recent addition to the various selective staining methods is the technique using restriction endonucleases to digest the metaphase chromosomes and subsequent staining by Giemsa (endonuclease/Giemsa technique). One of the endonucleases, AluI, which induces a characteristic modified C-band pattern is evaluated for its application in cancer cytogenetics using malignant lymphoid cells. The pattern obtained by AluI/Giemsa has been routinely useful in identifying some of the unusual markers that are difficult by routine banding. The centromeric regions are found to be far more heterogeneous by AluI resulting in frequent heteromorphic markers on several chromosomes. This has provided additional information to detect the donor cells in grafts after bone marrow transplantation.