The redistribution and trafficking patterns of cells to different anatomic sites throughout the body is important during cancer development and metastasis. Interest in the origin and fate of gastric cancer stem cells has recently arisen, as it may explain the underlying mechanism of cancer development. The ability to monitor the migration patterns of cancer stem cells is imperative to understanding the functional changes associated with the migration and proliferation of these cells. Here we detail a collection of techniques that include fluorescent in vivo imaging, X/Y FISH, and beta-galactosidase detection that are used for following labeled cells in vivo after adoptive transfer or transplant of donor cells for identifying the migration and engraftment of donor cells within the recipient.