Allogeneic hematopoietic cell transplantation in humans results in true biological chimeras. There is now accumulating evidence that besides Graft versus Host Disease (GvHD), there are also other consequences in the co-existence of two genetically distinct populations in the transplant recipient. First, epithelial cells with donor-derived genotype emerge. Second, epithelial tissues of the host acquire genomic alterations. The current review discusses existing data on these recently discovered phenomena and focuses on horizontal gene transfer between donor and recipient cells as a possible mechanism explaining and linking these phenomena.