The genetic predisposing factor for childhood retinoblastoma resides on the q14 band of human chromosome 13. However, a postulated second genetic event must take place for the disease to occur, which further research indicates involves inactivation of the remaining functional allele within 13q14. Our isolation of the gene within 13q14, called Rb, required creating a lambda-phage library that contained inserted fragments from human chromosome 13. One of the inserts, H3-8, detected a corresponding 1.8-kb HindIII fragment that was deleted in 2 of 37 retinoblastoma tumor DNAs. This suggested that the probed segment was linked to the Rb gene. A nearby probe, p7H30.7R, detected not only the human sequence but also a mouse homologue in a somatic cell hybrid carrying human chromosome 13. We used the p7H30.7R probe for RNA analysis to detect any transcripts in a retinal cell line. The analysis showed a 4.7-kb transcript in the tumor cell line but not in several retinoblastomas. We also failed to detect a transcript in four retinoblastoma and two osteosarcoma samples using a corresponding cDNA fragment termed p4.7R. We used this probe to analyze the DNA from a large group of retinoblastomas and osteosarcomas and found gross changes in genomic structure in approximately 30% of the tumor DNAs. The boundaries of homozygously deleted fragments were mapped. In the analysis of an osteosarcoma and a retinoblastoma we discovered that the endpoints of the deletions were within the confines of the genetic unit defined by the probe. This indicated that the target of inactivation was the segment under study and not a neighboring DNA sequence.