We have used chromosome-mediated gene transfer (CMGT) and whole cell fusion to derive human-mouse hybrid cells carrying reduced human chromosomes 11, by selecting for expression of the transforming H-ras 1 oncogene. To realize the full potential of these somatic cell genetic techniques as resources for enriched DNA probe isolation and the fine structure mapping of chromosomes, the nature of any molecular rearrangements that may accompany the process of DNA transfer must be understood. We have analyzed the long-range structure of our transgenomes by pulsed field gel electrophoresis (PFGE) and show here that, whereas during cell fusion several megabase pairs (Mb) of DNA can be transferred intact, multiple rearrangements of DNA accompany CMGT even in transgenomes where other methods of analysis gave no indication of such molecular scrambling.