To date, alkylthiol gold nanoparticles (AuNPs) have been widely used in electro-chromatographic separation techniques as a viable alternative to traditional stationary phases. This is mainly due to their stability, chemical inertness, ease of functionality, increased phase ratio, ability to form self-assembled monolayers. They also yield versatile stationary phases with highly specific targeted functionalities. At the nanoscale region, the chemical and physical properties of a molecule display different attributes to that of the parent molecules or material, hence these features can be harnessed in electro-driven chromatographic separations. Application areas illustrating the use of AuNPs in separation science continue to grow and expand to cover many different kinds of analysis. The last decade has witnessed a successful trend in miniaturisation of chemical separation systems toward the micro and nanoscale ranges. Nanoparticle-based stationary phases fit well with performing chemical separations on microfluidic and capillary platforms. In this review the theory of the use of alkylthiol gold nanoparticles in electro-chromatographic driven separation methods will be discussed. This will be followed by details of recent and selected applications showing alkylthiol gold nanoparticles in capillary electrophoretic and open-tubular electro-chromatographic separations. This review will focus solely on alkylthiol based gold nanoparticles, therefore other kinds of chemical moieties bonded to gold nanoparticles are outside the scope of this review. Finally the future outlook of this exciting technology will be outlined in some detail in the final section.