This article is dedicated to construction of the system of information security in automated data processing systems that function by analogy with the human immune system. The subject of this research is the development of the procedure for countering external intrusions of viruses, spam, and other destructive software programs in automated data processing systems. The object of this research is the systems of ensuring information security in automated data processing systems and human immune system. Methodological research on elaboration of the procedure for identification of intrusion is conducted via methods of artificial intelligence, systemic analysis, theory of neural and immune systems in the sphere of ensuring information security based on the achievements of systemic analysis and a systemic-conceptual approach towards information security in automated data processing systems. The main result lies in the developed general procedure for the functionality of the system of ensuring information security in countering external intrusions in the form of block-diagram and its description. The procedure is based on the idea of similarity in functionality of the mechanisms and procedures for protection against external intrusions in both, human immune system and automated data processing system, as well as drawing parallel between them. The main peculiarity of the developed procedure lies in its applicability to the accepted classification of the initial external environment of intrusion onto physical, information, field, and infrastructure environments. Such approach guarantees the novelty of the development from the perspective of constant updating of human immune system countering mechanisms to the external intrusions and its application for each environment in applicable to automated data processing systems.