Drosophila melanogaster offers a powerful system for the analysis of cell migration. In the embryo, -pluripotent cells of the mesodermal and endodermal primordia undergo epithelial-mesenchymal transitions and cell migration, while primordial germ cells migrate through an endodermal barrier to form the gonads. Visualisation of these migrations has traditionally been achieved by staining fixed embryos at different developmental stages or through live imaging of cells using tissue-specific expression of marker fluorescent proteins. More recently, photoactivatable fluorescence proteins have allowed the labelling of small groups of cells or single cells so that their migratory patterns and fate can be followed. By fusing the photoactivatable fluorescent protein to proteins that mark different subcellular components, it is now possible to visualise different aspects of the cells as they migrate. Here, we review previous studies of the migration of pluripotent embryonic cells and describe, in detail, methods for visualising these cells.