Fibroadenoma (FA) and phyllodes tumor (PT) of the breast are biphasic tumors composed of variable proportions of epithelial and stromal cells. We identified a case of synchronous FA and PT in the same breast mass. Using laser capture microdissection, loss of heterozygosity analysis was performed on these components to gain potential insight into the histogenetic relationship between FA and PT. Genomic DNA was analyzed at 10 microsatellite loci by polymerase chain reaction. Both tumors showed allelic loss at D7S522. In addition, phylloid tumor showed allelic loss at TP53 and D22S264, not observed in FA. Our data suggest that FA and PT are clonally related and allelic loss at TP53 and D22S264 may be implicated in the progression of FA to phyllode tumor.