OBJECTIVE Traditionally, tooth germ is observed by histological investigation with hematoxylin and eosin stain and information may loss during the process. The purpose of this study is to use multiphoton laser fluorescence microscopy to observe the developing tooth germs of mice for building up the database of the images of tooth germs and compare with those from conventional histological analysis. METHODS Tooth germs were isolated from embryonic and newborn mice with age of Embryonic Day 14.5 and Postnatal Days 1, 3, 5, and 7. RESULTS Comparison of the images of tooth germ sections in multiphoton microscopy with the images of histology was performed for investigating the molar tooth germs. It was found that various signals arose from different structures of tooth germs. Pre-dentin and dentin have strong second-harmonic generation signals, while ameloblasts and enamel tissues were shown with strong autofluorescence signals. CONCLUSIONS In this study, a novel multiphoton microscopy database of images from developing tooth germs in mice was set up. We confirmed that multiphoton laser microscopy is a powerful tool for investigating the development of tooth germ and is worthy for further application in the study of tooth regeneration.