The design of cryptographic and security protocols for new scenarios and applications can be computationally expensive. Examples of these can be sensor or mobile ad-hoc networks where thousands of nodes can be involved. 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 two aspects are critical: the genome definition and the evaluation function. We discuss how security protocols can be represented as binary strings and can be interpreted as security protocols; moreover we define several basic criteria for evaluating security protocols. Finally, we present the software we developed for generating secure communications protocols and show some examples and obtained results.