Interphase cytogenetics was used to investigate the clonal origin of bone marrow (BM) cells, peripheral blood (PB) cells, and in vitro cultured progenitor cells of five patients with acute myeloid leukemia (AML) and myelodysplasia (MDS). A new in situ hybridization (ISH) technique was used to examine the origin of the progenitor cells. Two patients with respectively, trisomy 8 and polyploidy as ISH marker were studied both at presentation and during remission. At presentation, the in vitro cultured clusters of both cases appeared diploid. Therefore, despite the abnormal growth patterns, the cultured progenitors could have been residual normal cells. Alternatively, they could have originated from a preleukemic clone with a normal karyotype. In both cases abnormal BM and/or PB cells (less than 6%) were detected with ISH during remission, indicating partially or completely clonal remissions in these patients. Both patients have relapsed. One patient with trisomy 10 as ISH marker was analyzed during myelodysplastic phase and after progression to AML. On both occasions, abnormally appearing clusters were cultured. However, only part of the clusters carried trisomy 10. The presence of a subclone characterized by trisomy 10 and an abnormally growing (pre)leukemic clone without trisomy 10 may explain this observation. Monosomy 1 and 17 were respectively used as ISH markers in two other AML patients. All in vitro cultured clusters carried the numerical abnormality. Long-term liquid cultures of these leukemias were performed for 10-20 days. In both cases, no residual normal clonogenic cells could be detected. Therefore, the selective growth advantage of normal progenitor cells in long-term marrow cultures could not be demonstrated in these two patients with leukemia. This paper illustrates the usefulness of ISH to study the biology of AML at the clonogenic level during preleukemic phase, active disease, remission, and under in vitro culture conditions. It is a sensitive technique which allows individual analysis of large numbers of small aggregates and single cells in culture.