A new approach for the botnet detection based on multi-agent system is proposed. The structure and main principles of antiviral agents' functioning within multi-agent system is developed. The principles of communication between the agent's units before and after attack on the computer system were developed. Software for realisation of antivirus multi-agent system on proposed techniques was developed. It shows growth of accuracy by 3-5% in comparison with known antivirus software. This approach is the basis for the development of new informational technology of antivirus diagnosing based on multi-agent system in order to increase the accuracy for the botnet detection in computer systems. Keywords: botnet, Trojan, worm-virus, antivirus detection, multi-agent system, agent, sensor, fuzzy logic.