Recently, the information technology and its various branches, including information security have been under focus. Thus, the need for having efficient cryptographic algorithms that can simultaneously satisfy different goals such as the simple implementation, high speed and high security is felt much more than the past. Because of having different mentioned aspects, stream ciphers have many applications in cryptosystems. Security analysis of the stream ciphers is also one of the subjects that are getting a lot of attention. There are two general types of attacks on stream ciphers including key recovery and distinguishing attacks. In a key recovery attack, the goal of the attack is to extract some information about the key but in a distinguishing one the attacker tries to distinguish between the output of the stream cipher and a real random sequence. In this thesis, a brief introduction of the stream cipher and some important attacks on them are described and then distinguishing attack and hypothesis testing, as an important tool for applying this attack, are explained in detail. After that, we look at a practical situation in which a distinguisher is used to derive information about the plaintext. Applying the distinguishing attack on different structures of stream ciphers such as combining and filter generators and clock controlled generators are described and a new attack on systems with linear state updating is presented. Finally, attacks on basic algorithms including ASG and summation generator as well as the new ciphers MAG and WG are presented. Also, the complexities of the proposed attacks are compared with the previous attacks on these ciphers. Keywords Stream Ciphers, Distinguishing Attacks, Key Recovery, WG, MAG