Stream ciphers are fast cryptographic primitives to provide confidentiality of electronically transmitted data. They can be very suitable in environments with restricted resources, such as mobile devices or embedded systems. Practical examples are cell phones, RFID transponders, smart cards or devices in sensor networks. Besides efficiency, security is the most important property of a stream cipher. In this thesis, we address cryptanalysis of modern lightweight stream ciphers. We derive and improve cryptanalytic methods for different building blocks and present dedicated attacks on specific proposals, including some eSTREAM candidates. As a result, we elaborate on the design criteria for the development of secure and efficient stream ciphers. The best-known building block is the linear feedback shift register (LFSR), which can be combined with a nonlinear Boolean output function. A powerful type of attacks against LFSR-based stream ciphers are the recent algebraic attacks, these exploit the specific structure by deriving low degree equations for recovering the secret key. We efficiently determine the immunity of existing and newly constructed Boolean functions against fast algebraic attacks. The concept of algebraic immunity is then generalized by investigating the augmented function of the stream cipher. As an application of this framework, we improve the cryptanalysis of a well-known stream cipher with irregularly clocked LFSR's. Algebraic attacks can be avoided by substituting the LFSR with a suitable nonlinear driving device, such as a feedback shift register with carry (FCSR) or the recently proposed class of T-functions. We investigate both replacement schemes in view of their security, and devise different practical attacks (including linear attacks) on a number of specific proposals based on T-functions. Another efficient method to amplify the nonlinear behavior is to use a round-based filter function, where each round consists of simple nonlinear operations. We use differential methods to break a reduced-round version of eSTREAM candidate Salsa20. Similar methods can be used to break a related compression function with a reduced number of rounds. Finally, we investigate the algebraic structure of the initialization function of stream ciphers and provide a framework for key recovery attacks. As an application, a key recovery attack on simplified versions of eSTREAM candidates Trivium and Grain-128 is given.