In situ hybridization for Y heterochromatin was used to detect loss of the Y chromosome in interphase cells of three elderly male patients who presented with pancytopenia, hypocellular marrow with mild to moderate dysplasia, and variable numbers of 45,X, -Y or -G marrow metaphases. The percentages of Y-negative peripheral blood mononuclear cells from the patients (1.5-12.5%) exceeded that of elderly males (0.4 +/- 0.3%) and young males (0.03 +/- 0.1%) without hematologic disorders, but the percentages of Y-negative phytohemagglutinin-stimulated cells from the patients were within the range of normals. All three patients had Y-negative granulocytes (2.1-16.7%), while none of 34 males without hematologic disease had any Y-negative granulocytes. These results suggested the presence of a myeloid clone with loss of Y. One patient developed acute nonlymphocytic leukemia with 38.4% Y-negative marrow cells. Morphologically, the Y-negative cells were blasts. The other two patients remained stable or improved over the period of treatment and observation despite persistence of the cytogenetic finding and dysplastic changes. Loss of the Y chromosome in excess of normal as determined by in situ hybridization may be an indicator of a clonal disorder in males with pancytopenia, but it is not necessarily a marker of poor prognosis.