Fluorescent proteins have revolutionized in vivo biology. Due to their intrinsic brightness, multiple colors, and ease of genetic manipulation, fluorescent proteins have been demonstrated to be the reporters of choice for in vivo imaging. The present report reviews applications of fluorescent proteins for imaging cancer progression, gene expression, angiogenesis, stem cells, bacterial infection, Leishmania infection, and asthma, at the cellular and subcellular level in live mice. With fluorescent-protein-expressing cells and a highly sensitive small animal imaging system, cellular and subcellular dynamics can now be observed in live mice in real time. Such imaging possibilities can provide new visual targets for novel drug therapy. Fluorescent proteins thus enable both micro as well as macro imaging technology and thereby provide the basis for the new field of in vivo cell biology.