Cytogenetic analysis was performed on B-cell mitogen-stimulated cells from 36 patients with symptomatic hairy cell leukemia. Evaluable metaphases were achieved from 30 patients, and (67%) showed clonal abnormalities. Recurrent chromosomal aberrations involving chromosomes 1, 2, 5, 6, 11, 19, and 20 were found. The abnormalities were mostly deletions and inversions, whereas translocations and numerical abnormalities, except trisomy 5, were rare. Fourteen patients showed multiple clones, which mostly were unrelated and found in different combinations in individual cells. Cells with non-clonal abnormalities identical to those found in clonal changes in other patients were common. Chromosome 5 was involved in clonal aberrations in 12 of 30 (40%) patients, most commonly as trisomy 5 (n = 4), or pericentric inversions (n = 6) and interstitial deletions (n = 4) involving band 5q13. Three patients showed two and 1 patient three different clones that involved chromosome 5. In addition, 1 patient had a rare constitutional inversion of chromosome 5 with breakpoints at p13.1 and q13.3. Pericentric inversions and interstitial deletions of chromosome 2 occurred clonally in 4 patients (13%) and in single cells of another 6 patients. Deletions of chromosome 1 at band q42 was found in 5 patients, and 1 patient had a translocation between 1q42 and a supernumerary chromosome 5. Deletions of 6q and 11q were similar to those commonly found in other lymphoproliferative disorders. Trisomy 5, structural abnormalities involving the pericentromeric regions of chromosomes 5 and 2, and 1q42 abnormalities were findings distinguishing the karyotypes in hairy cell leukemia from those of other hematologic malignancies.