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Objective The confocal laser scanning microscope represents an effective tool for studying biological samples stained for fluorescence observation. In this study we have used the confocal microscope to analyze ghost cells in calcifying cystic odontogenic tumors. Study design Specimens from 15 calcifying cystic odontogenic tumor cases were stained with hematoxylin and eosin, and scanned by a confocal laser scanning microscope to generate optically sectioned images. Results All of the analyzed samples presented autofluorescent cells that were identified as ghost cells. The degree of autofluorescence intensity was variable and may be a result of the presence of hard keratin. Conclusion The confocal laser scanning microscope may be of help in analyzing and defining the nature and extent of keratinization processes in calcifying cystic odontogenic tumor ghost cells.