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The paper deals with test results of the influence of Penicillium chrysogenum and Cladosporium herbarum fungi on the mechanical and sorption properties of cement mortars CEM I and the mortars modified by polymers. The corrosion processes were identified by chemical oxygen demand (COD) analysis, by the aid of a scanning microscope with an X-ray microanalyser and by mercury porosimetry. The results presented show a high concentration of the fungi in the mortars, especially in the materials modified by polysiloxane and acrylic polymers. The presence of the fungi greatly influences the useful properties of cement materials. The high growth of these microorganisms significantly influences the mass moisture and absorbability as well as flexural strength, which is strictly connected with these properties. The actions of the filamentous fungi resulted in two opposing processes: the unsealing of the structure and deposition of corrosion products.