We demonstrate noninvasive, high-resolution multiphoton tomography of nestin-expressing stem cells of hair follicles in living transgenic nude mice. An imaging system comprised of a compact femtosecond laser, 3D scan head mounted on a flexible mechano-optical articulated arm for simultaneous intra-tissue fluorescence and second harmonic detection (SHG) detection was used. This noninvasive method enables long-term in vivo tracking of intra-tissue stem cells in living animals. Multiphoton animal sectioning with subcellular resolution can visualize the real-time behavior of single stem cells in their native tissue microenvironment.