The histogenesis of polygonal cells and cuboidal cells in so-called pulmonary sclerosing hemangioma remains unclear. To understand their histogenesis, polygonal and cuboidal cells were obtained from pulmonary sclerosing hemangioma tissue using a laser capture microdissection technique. Genomic DNA and total RNA were extracted and mRNA levels of cytokeratin, epithelial membrane antigen, vimentin, surfactant protein B, thyroid transcription factor-1, synaptophysin, and chromogranin-A were analyzed by RT-PCR. DNA was digested with the methylation-sensitive enzymes HhaI or HpaII, followed by nested PCR of the androgen receptor and phosphoglycerate kinase genes. Samples with polymorphisms were identified and a clonality analysis was performed. The cytokeratin, epithelial membrane antigen, and surfactant protein B genes were clearly expressed in cuboidal cells, while the vimentin and synaptophysin genes were clearly expressed and the epithelial membrane antigen gene was weakly expressed in polygonal cells. Thyroid transcription factor-1 was expressed in both cell types, while neither cell type expressed chromogranin-A. Clonality analysis showed the same loss of allele in both cell types (clonality ratio=0) or an unbalanced methylation pattern (clonality ratio<0.25). Polygonal and cuboidal cells in pulmonary sclerosing hemangioma exhibited a uniform pattern of monoclonality, indicating that both cell types are highly likely to originate from a common precursor. The differences in their morphological phenotype might result from their different mature status.