Following transplantation of green fluorescent protein (GFP)-labeled bone marrow (BM) into irradiated, wild-type Sprague-Dawley rats, propagated GFP(+) cells migrate to adipose tissue compartments. To determine the relationship between GFP(+) BM-derived cells and tissue-resident GFP(-) cells on the stem cell population of adipose tissue, we conducted detailed immunohistochemical analysis of chimeric whole fat compartments and subsequently isolated and characterized adipose-derived stem cells (ASCs) from GFP(+) BM chimeras. In immunohistochemistry, a large fraction of GFP(+) cells in adipose tissue were strongly positive for CD45 and smooth muscle actin and were evenly scattered around the adipocytes and blood vessels, whereas all CD45(+) cells within the blood vessels were GFP(+). A small fraction of GFP(+) cells with the mesenchymal marker CD90 also existed in the perivascular area. Flow cytometric and immunocytochemical analyses showed that cultured ASCs were CD45(-)/CD90(+)/CD29(+). There was a significant difference in both the cell number and phenotype of the GFP(+) ASCs in two different adipose compartments, the omental (abdominal) and the inguinal (subcutaneous) fat pads; a significantly higher number of GFP(-)/CD90(+) cells were isolated from the subcutaneous depot as compared with the abdominal depot. The in vitro adipogenic differentiation of the ASCs was achieved; however, all cells that had differentiated were GFP(-). Based on phenotypical analysis, GFP(+) cells in adipose tissue in this rat model appear to be of both hematopoietic and mesenchymal origin; however, infrequent isolation of GFP(+) ASCs and their lack of adipogenic differentiation suggest that the contribution of BM to ASC generation might be minor.