Various kinds of cell types exist in the body and communicate with each other. Although there have been many previous studies of cellular dynamics in several organs, most involved conventional methods such as histological analysis and flow cytometry. These methods cannot observe dynamic cell movement in living tissues. Recently, rapid development of multiphoton microscopy has enabled us to visualize cellular dynamics deep inside living tissues and organs without thin sectioning. Focal excitation of fluorophores by simultaneous attack of multiple (normally ‘two’) photons generates images with high spatial resolution, and use of near‐infrared lasers for multiphoton excitation allows for the penetration of thicker specimens. Moreover, the minimized photobleaching and toxicity associated with multiphoton techniques allow for the imaging of living specimens for extended observation periods. Here, we focus on recent findings using intravital multiphoton imaging of dynamic biological systems, and in particular, bone homeostasis. This approach could be beneficial for understanding the mechanisms underlying dynamic biological systems, and thus useful for evaluating the efficacy and effect of novel drugs currently in development.