Abstract C3H fibroblasts transformed in vitro with SV40 were adapted to in vivo growth. Several clones were isolated from a single, highly oncogenic tumor and those that displayed oncogenic potential also no longer expressed the H-2Kk molecule. Using the technique of Southern blot hybridization, the H-2 genes and integrated SV40 sequences present in the genomic DNA of several of these clones have been examined and compared with both the parent line and normal liver genomic DNA from C3H mice. All H-2Kk negative clones had altered H-2 genes that appeared as a gain and, depending on the restriction endonuclease, loss of hybridizing fragments compared to normal C3H DNA. A 5.5-kb fragment missing from the Sstl digests of the H-2Kk negative variants was mapped to the H-2Kk region of the major histocompatability complex with the use of congenic mice. This provided direct evidence that a mutation had occurred in the H-2Kk region. The integrated SV40 sequences were similar to those already seen in other SV40 transformed cells and not closely linked to any of the H-2 genes. There was no indication that the H-2 mutation was caused by integration of SV40.