Bone marrow cells can engraft in the liver and differentiate into a variety of cell types including hepatocytes and myofibroblasts. This chapter describes how, after transplantation of male bone marrow into female recipients, cells of bone marrow origin (male) can be identified in the female liver by virtue of detection of the Y chromosome by the technique of in situ hybridisation (ISH). Furthermore, ISH for Y chromosome detection can be combined both with immunohistochemistry (IHC) to identify phenotype and with ISH for mRNA to demonstrate function. Additionally, we show that bone marrow-derived cells can be identified in the liver without prior sex-mismatch bone marrow transplantation, identifying instead the BCR:ABL fusion gene that is present in all such cells in almost all patients suffering from chronic myelogenous leukaemia (CML).