Cytogenetic changes are of pivotal prognostic significance in patients with de novo acute lymphoblastic leukemia (ALL). However, in some cases leukemic blasts can harbor gene lesions on a submicroscopic level without evidence of a corresponding abnormality by conventional cytogenetic studies. This can result in failure to recognize chromosomal abnormalities and inappropriate evaluation with respect to therapy assignments. To study the discrepancy in the detection of deletions of the short arm of chromosome 9 and deletions of tumor suppressor genes p15/p16/p14 on chromosome 9p21, we analyzed bone marrow samples from 92 patients with ALL both by cytogenetic analysis and by Southern blot. In 41 patients (45%), we found deletions of p15/p16/p14, which were homozygous in 27 and hemizygous in 14. Cytogenetic analysis demonstrated abnormalities of the short arm of chromosome 9 in the form of 9p- or del(9p21-22) in only 5 of the 41 patients (12%). Only 2 of 51 patients without gene deletions as detected by Southern blot revealed a 9p- abnormality, which was found only in a subpopulation of the cells. We demonstrate that deletions of the p15/p16/p14 genes on chromosome 9p21 are more frequent than indicated by cytogenetic analysis. Molecular techniques in addition to cytogenetic studies are necessary to detect otherwise-unrecognized genetic lesions of the short arm of chromosome 9.