Along with the development of the Internet and information technologies, broadening of the scope of intellectual property rights and occurrence of the intellectual leverage effect with regard to the use of knowledge in preparing innovative products and services, it is possible to observe a growth in the importance of intangible assets in building strategic advantage of business entities. Important is that effective organisation management requires skilful use of information reflecting functioning of all subsystems of a given institution, including the functional systems (such as communication system and knowledge management system classified as intangible assets). Such knowledge is provided by an internal audit being a tool including independent and objective analysis of efficacy and efficiency of processes, which is used first of all to facilitate these processes. The purpose of this study is thus to present the possibility of using the audit in business practice of intangible assets management with regard to communication system and knowledge management system.