We report results from the study of 33 children with acute lymphoid (25) and myeloid (8) leukaemia. Karyotyping of bone marrow cells is an important step for the precise diagnosis and for the choice of the adequate treatment in leukaemic patients. Twenty six patients were examined in the time of diagnosis and seven in relapse. The cytogenetic analyses were performed on 24-hours bone marrow cells cultured in RPMI 1640 according to the standard methods. GTG banding technique revealed clonal karyotypic abnormalities in 45% (15) samples. Cytogenetic findings were confirmed by fluorescence in situ hybridization (FISH) method. Comparative genomic hybridization (CGH) was used on bone marrow samples obtained from this patients in time of diagnosis or relapse. CGH showed new DNA copy number changes in 70% (23) patients. For the first time we were tested the modification of CGH. We show examples of submicroscopic chromosomal imbalances being detected with this high resolution CGH technique (HR-CGH). By HR-CGH we detected new chromosomal aberation in more than 75% cases. Here we present comparing among GTG-band karyotyping, CGH and HR-CGH results.