Fluorescence in situ hybridization (FISH) allows detection of specific chromosomal aberrations in abnormal cells. In chronic myeloid leukaemia (CML) and acute lymphoblastic leukaemia (ALL), chromosomal abnormalities have been found in the bone marrow of children and adults. Detection of a number of malignant cells carrying specific aberrations after bone marrow transplantation is of great importance. FISH techniques with the use of specific probes for CML and ALL could detect a minimal residual disease and mixed chimerism after bone marrow transplantation.