The new model of the computer system diagnosing process for botnet presence in the corporate area network is proposed. It is based on the use of multi-agent system. The new botnet detection technique based on multi-agent system with the use of fuzzy logic is proposed. The detection is performed in the situations of priori uncertainty of the botnet presence in the corporate area network with taking into account the botnet demonstrations in the several computer systems available in the network. Fuzzy expert system for making conclusion about botnet presence degree in computer systems is developed. Key words: bot, botnet, antiviral diagnosis, model of antiviral diagnosis process, antiviral agent model, multi-agent system model, fuzzy logic, expert system.