Abstract Recently, a new type of attack called Advanced Persistent Threat (APT) headline the news frequently. Different from other type of attacks, APT often has specific targets given sufficient fund support, and the attack can exist for a long period of time without being discovered. No single current protection approach alone can efficiently defeat APT, and thus research effort is required to further investigate this area. In this paper, we discuss the concepts of APT as well as the newest trends on how to efficiently detect and neutralize these hidden threats. A brief overview of eight accepted papers in our Special Issue on Advanced Persistent Threat is presented. Finally, we conclude this paper by highlighting the key points and summarizing the paper.