Confocal laser scanning microscopy (CLSM) represents a recent acquisition in the study of biological samples stained for fluorescence observation. Particularly, this technique allows a bidimensional investigation of tissues and cells with the possibility to elaborate a three-dimensional model. The aim of this study is the use of this technique, as a complementary and not substitutive application of the histological examination, for the morphological and histopathological analysis in a case of mixed complex-composed odontoma. The analyzed specimen has been surgically removed in the superior frontal region in a 12 year-old boy and submitted to conventional histopathological analysis. The specimen, hematoxylin-eosin stained, has been subsequently submitted to confocal laser scanning microscopic analysis in autofluorescence by using a Nikons C1 system. This analysis has underlined not visible aspects in traditional optical microscopy, such as the mineralization of hard tissues and the morpho-structural organization of the cellular component. The presence of enamel and dentin may be observed in the different phases of odontogenesis with clear fluorescence gradients determined by the different mineralization degrees. Thus, the odontogenetic components appear strongly autofluorescent in the classical follicular configuration. Three-dimensional reconstruction is made possible by the acquisition of serial bidimensional images that are subsequently analysed by using a specific software device. This study shows the confocal laser scanning microscopy versatility in the analysis of odontogenic neoplasms with production of mineralized tissues.