Public universities in the Czech Republic register every year hundreds of internally generated patents for inventions, utility models or industrial designs, prototypes or functional. Internally generated intangible assets are the subject of evaluation and accounting. As such, it should be recorded in the balance sheet of the entity in the category of intangible assets and depreciated progressively. The aim of this work is to determine whether the internally generated intangible assets are recognized in the balance sheets of universities. Executed comparison of the research' results of universities reported to the Council for Research, Development and Innovation with the balance sheet of universities in 2011, it was found that 95% of universities does not show in their balance sheets internally generated intangible assets, which are however presented to the Council for research, development and innovation as the research results of public universities. It is evident, that public universities dispose with large amount of intangible assets whose existence is not declared in the financial statements. Their accounting doesn't provide the true picture of the assets of these economic entities.