The interaction of Aspergillus fumigatus with human bronchial mucosa in an organ culture model, with an air-mucosal interface, was studied. A. fumigatus conidia were inoculated onto the organ culture tissues and incubated for 24 h. At each time point (1, 6, 12, 18 and 24 h), after the measurement of ciliary beat frequency (CBF) of bronchial epithelial cells, adherence and invasion of the epithelium by A. fumigatus conidia (and hyphae), as well as structural changes of the epithelium, were investigated by scanning and transmission electron microscopy. This study demonstrated that A. fumigatus caused damage to the bronchial epithelium that was associated with CBF slowing. In addition, the study demonstrated that some of the conidia of A. fumigatus were internalized within ciliated and non-ciliated epithelial cells, some conidia were located within the intercellular spaces of the epithelium, and that hyphae penetrated through both intercellular and intracellular spaces of the epithelium. These findings suggest there might be at least three pathways by which Aspergillus invades the bronchial mucosa: (1) penetration of hyphae through the intercellular spaces in the epithelium; (2) direct penetration of hyphae through epithelial cells; and (3) internalization of conidia within epithelial cells.