We applied a differential cloning procedure, the in-gel competitive reassociation (IGCR) method, to clone altered genomic sites from the whole genomes of renal cell carcinoma cells. After four rounds of IGCR, we obtained from two patients libraries enriched 1000- and 2500-fold for differential DNA fragments specific to allelic changes in renal cell carcinoma. In these libraries, we found differential fragments of single-copy sequences as well as repetitive sequences. The fragments exhibited allelic loss, restriction-fragment-length polymorphism, size changes, and changes in the copy number, and common allelic losses were also detected in the cancer tissues from several renal cell carcinoma patients. Some of the clones showed changes in the repeat length of microsatellites. One third (seven of 22) of the clones exhibiting these changes were mapped to chromosomes 8 or 9. Decreases in the copy numbers of mitochondrial DNA and satellite I were observed in 13 of 17 and seven of 16 renal cell carcinoma patients, respectively. This suggests that the IGCR method can be used to clone DNA fragments with various structural changes from the whole genomes of cancer tissues.