Polycythemia vera (PV) is believed to represent a clonal trilineage myeloaccumulative hematopoietic disorder. This study was undertaken to estimate for the first time the proportion not only of the neoplastic clone but also of clonal and residual nonneoplastic CD34(+) progenitor cells. Chromosomal abnormalities, including trisomy 8 or 9, are phenomena associated in about 20% of PV patients. Therefore, we screened peripheral blood (PB) mononuclear cells of PV patients in the chronic phase of the disease and looked for chromosomal abnormalities performing comparative genomic hybridization. Two of the ten patients revealed cytogenetic changes, including trisomy 8 or 9. To quantify the proportion of cytogenetic abnormal cells in these patients, we applied fluorescence in situ hybridization (FISH) technique on immunomagnetically enriched cell fractions. Ninety percent of the mononuclear cells and up to 79% of PB-derived CD34(+) progenitor cells presented three signals for chromosome 8 or 9. The diagnostic value of FISH to detect trisomies in trephine biopsies was then tested in all patients under study. Although the probability to detect FISH signals in a certain section plane is reduced, constantly 10-15% of the cells revealed three signals. Concerning the CD34(+) progenitor cell pool, a distinct nonclonal population exists in these patients. Our data underline the stem cell character of PV and additionally quantify the proportion of clonal CD34(+) progenitor cells for the first time. The finding of a distinct, not aberrant, CD34(+) progenitor cell population in chronic phase PV may offer perspectives in treatment of the disease. Finally, FISH analysis of bone marrow biopsies can be helpful to consolidate diagnosis of early PV.