The main goal of this paper is to expose the community to past achievements and future possible uses of Instruction Set Extension (ISE) in security applications. Processor customization has proven to be an effective way for achieving high performance with limited area and energy overhead for several applications, ranging from signal processing to graphical computation. Concerning cryptographic algorithms, a large body of work exists on speeding up block ciphers and asymmetric cryptography with specific ISEs. These algorithms often mix nonstandard operations with regular ones, thus representing an ideal target for being accelerated with dedicated instructions. Tools supporting automatic generations of ISEs demonstrated to be useful for algorithm exploration, while secure instructions can increase the robustness against side channels attacks of software routines. In this paper, we discuss how processor customization and the relative tool chains can be used by designers to address security problems and we highlight possible research directions.