We evaluated the usefulness of in situ hybridization (ISH) with chromosome specific DNA probe on paraffin sections of bone marrow aspirates. Twenty cases of hematopoietic malignancy and eight control cases of non-hematopoietic malignancy were examined with centromere-specific probes for chromosomes 8 and 17. In the eight control cases, the mean rates of cells with more than three hybridization signals were 1.13 (2SD = 1.90) for chromosome 8, and 0.88 (2SD = 2.25) for chromosome 17. The mean rates plus 2SD were 3.03 for chromosome 8, and 3.19 for chromosome 17. Therefore, we defined cases of more than 4.0% of cells showing more than three hybridization signals per nuclei as having a numerical abnormality (trisomy). We compared these results with conventional cytogenetic results by karyotype analysis. In twenty hematopoietic malignancy cases, three cases demonstrated trisomy 8 by ISH. Two cases also demonstrated this abnormality by karyotype analysis, but one case showed no abnormality by karyotype analysis. While trisomy 17 detected in one case that did not demonstrate numerical abnormality, only structural abnormality by karyotype analysis. The rate of discrepancy between results of ISH analysis and those of karyotype analysis was only 5% (2/40) for both chromosomes. In five cases, re-examinations were performed within three months. In one case, we could not obtain adequate material for karyotype analysis. However, this case showed trisomy 8 by ISH. Structural chromosomal abnormalities such as translocation or deletion could not be detected by this ISH analysis with centromere-specific probes. However, this method has the advantage result that we can perform retrospective assessments, do not need to culture cell, and can compare with pathological findings. Thus, we conclude that ISH analysis with paraffin sections of bone marrow aspirates will provide more useful information by combining ISH analysis and karyotype analysis.