Botnet is most widespread and occurs commonly in today‘s cyber attacks, resulting in serious threats to our network assets and organization’s properties. Botnets are collections of compromised computers (Bots) which are remotely controlled by its originator (BotMaster) under a common Command-and-Control (C&C) infrastructure. They are used to distribute commands to the Bots for malicious activities such as distributed denial-of-service (DDoS) attacks, spam and phishing. Most of the existing Botnet detection approaches concentrate only on particular Botnet command and control (C&C) protocols (e.g.,IRC,HTTP) and structures (e.g., centralized), and can become ineffective as Botnets change their structure and C&C techniques. In this book at first we provide taxonomy of Botnets C&C channels and evaluate well-known protocols which are being used in each of them. Then we proposed a new general detection framework which currently focuses on P2P based and IRC based Botnets. This proposed framework is based on definition of Botnets. Botnet has been defined as a group of bots that perform similar communication and malicious activity patterns within the same Botnet.