The design of cryptographic and security protocols for new scenarios and applications can be computationally expensive. Examples of these can be sensor or mobile adhoc networks and electronic voting or auctions applications. In such cases, the aid of an automated tool generating protocols for a predefined problem can be of great utility. This work uses the Genetic Algorithms (GA) techniques for the automatic design of security networked protocols. When using GA for optimizing protocols the evaluation function is critical. We discuss how can be defined several basic criteria for evaluating security protocols and present some examples for evaluation of different protocols.