Security protocols are predefined sequences of message exchanges. Their uses over computer networks aim to provide certain guarantees to protocol participants. The sensitive nature of many applications resting on protocols encourages the use of formal methods to provide rigorous correctness proofs. This dissertation presents extensions to the Inductive Method for protocol verification in the Isabelle/HOL interactive theorem prover. The current state of the Inductive Method and of other protocol analysis techniques are reviewed. Protocol composition modelling in the Inductive Method is introduced and put in practice by holistically verifying the composition of a certification protocol with an authentication protocol. Unlike some existing approaches, we are not constrained by independence requirements or search space limitations. A special kind of identity-based signatures, auditable ones, are specified in the Inductive Method and integrated in an analysis of a recent ISO/IEC 9798-3 protocol. A side-by-side verification features both a version of the protocol with auditable identity-based signatures and a version with plain ones. The largest part of the thesis presents extensions for the verification of electronic voting protocols. Innovative specification and verification strategies are described. The crucial property of voter privacy, being the impossibility of knowing how a specific voter voted, is modelled as an unlinkability property between pieces of information. Unlinkability is then specified in the Inductive Method using novel message operators. An electronic voting protocol by Fujioka, Okamoto and Ohta is modelled in the Inductive Method. Its classic confidentiality properties are verified, followed by voter privacy. The approach is shown to be generic enough to be re-usable on other protocols while maintaining a coherent line of reasoning. We compare our work with the widespread process equivalence model and examine respective strengths.