The feasibility of using molecular hybridization techniques for the detection of malignant clones that contain numerical chromosomal abnormalities was tested in clinical specimens from patients who had hematologic malignancies. A biotinylated DNA probe specific for chromosome 9 was used for in situ hybridization to interphase and terminally differentiated cells, and fluoresceinated avidin or avidin followed by biotinylated alkaline phosphatase was used for probe detection. In a blinded analysis of ten clinical samples from patients with hematologic malignancies and cytogenetically documented monosomy 9 or trisomy 9, the abnormality was identified correctly in each of five cases of monosomy 9 and five cases of trisomy 9. In two cases of trisomy 9, the detection of this numerical chromosomal abnormality in nuclei of segmented neutrophils permitted the deduction that some granulocytic cells were derived from the abnormal clone, but were still capable of terminal differentiation. Analysis of the position of the probe signal in such nuclei did not disclose any ordered localization of the chromosome 9 homologues with respect to segmentation. These results demonstrate that interphase cytogenetic analysis is feasible in peripheral blood and bone marrow specimens, and that this technique may be a useful adjunct to conventional cytogenetic analysis for the clinical management of patients with hematopoietic malignancies.