In this study, 27 malignant cell lines, including leukemias, gliomas, and lung and bladder carcinomas were screened for homozygous deletions of the putative tumor suppressor gene p16 (MTS1/CDK4I/CDKN2) and other markers within the chromosome 9p21 region; these include the genes for interferon-alpha1 (IFNA1), interferon-beta1 (IFNB1), methylthioadenosine phosphorylase (MTAP), and two microsatellite markers, D9S171 and D9S169. The purpose of this study was to determine the incidence of codeletion of these markers. Screening for homozygous deletions was carried out using direct polymerase chain reaction of genomic DNA, or, in the case of MTAP, a functional enzyme assay. Of these cell lines, 14 (52%) were found to have homozygous deletions of the p16 gene. Two of the 14 p16-negative cell lines (14%) were found to have homozygous deletions within the p16 domain but but no other 9p21 marker. MTAP was codeleted in 12 of the 14 p16-negative cell lines (86%), whereas IFNA1 was codeleted with p16 in eight of these lines (57%); IFNB1 was codeleted in five (36%) of the p16-deleted cell lines. The D9S171 marker, which may lie greater than 3 cM centromeric to p16, is codeleted in three cell lines (21%); the D9S169 marker, which maps even further toward the centromere, was codeleted in only one cell line (7%). Loss of any 9p21 marker, e.g., MTAP or IFNA1, were invariable predictors of the loss of the p16 gene. In addition, loss of IFNA1 always predicted a loss of MTAP (eight of eight cell lines), although loss of MTAP did not always predict a loss of IFNA1 (four of 12 MTAP-deleted cell lines did not have homozygous deletions of IFNA1). Thus loss of nearby genes occurs in a high percentage of cell lines that bear homozygous deletions of the p16 locus. Codeletion of MTAP or IFN in p16-negative malignant cells is of interest, as loss of these genes may influence the biologic behavior of these cells and render them susceptible to certain therapeutic approaches.