We employed the arbitrarily primed polymerase chain reaction (AP-PCR), which is a PCR-based genomic fingerprinting technique, to detect novel genetic alterations in human astrocytomas. DNA fingerprints generated by arbitrary primers were compared in normal lymphocytes and tumor tissues from the same individuals. We cloned and sequenced an AP-PCR band showing a greatly decreased intensity in tumor tissue DNA, relative to normal. Southern blot showed that this sequence was homozygously deleted in the tumor cell genome. Semiquantitative PCR analysis further showed significant decreases of signals in seven of 24 tumors, consistent with homozygous deletion of this sequence. The deleted sequence was localized to chromosome region 6p21.1 by the fluorescence in situ hybridization method. Microsatellite analysis also showed frequent allelic loss of this locus compared to neighboring loci in astrocytoma tissues. These results suggest the presence of a novel tumor suppressor gene at the 6p21.1 locus.