Abstract Aspergillus awamori was cultivated in shake flask cultures and in stirred tank reactors on synthetic medium and on complex medium, (with wheat bran substrate), respectively, and samples were taken at different cultivation times. The filamentous mycelia and pellets of the fungus were analyzed using four different techniques: transmission electron microscopy (TEM), electron spectroscopic imaging (ESI), electron energy loss spectroscopy (EELS) and immunocytochemical investigations. The ultrastructure of A. awamori and the colonization and decomposition of the wheat bran by the fungus were determined as a function of the cultivation time. The xylanase concentration in the cytoplasm and cell wall of the fungus was high during the first phase of the cultivation and it gradually decreased due to its secretion. At the same time the xylanase concentration increased on the surface of the solid substrate as well as in the cultivation medium. The variation of the local distribution of the enzyme xylanase during the cultivation was determined as well. It is shown how the fungus penetrates and decomposes the wheat bran. Phosphorous and sulfur inclusions, determined with ESI and EELS, were found in the vacuoles.