The article deals with the task of the security assessing of big data systems. The authors define the main features of big data systems as an object of security assessment and analyze the known methods of assessment, including methodologies for assessing the security of information systems. Based on the results obtained, a new method of assessment is proposed, taking into account such factors as the state of the access control system in the considered heterogeneous systems and the number of privileged users. A mathematical formalization of the assessment is proposed, the main stages of its implementation are described, and a test case is presented