Electrophoresis is a standard technique used in medical laboratories and research institutions worldwide, for DNA, RNA and protein analysis. Various methodologies and techniques have been developed over the past decades. The common ground used in all approaches is the separation of molecule particles based on their movement on a substrate under the existence of an electric field. Relevant research is assisted by the advancement of technology and focuses on the development of innovative and fully automated electrophoresis systems that use robotic systems and advanced programming techniques. To this extent, the proposed paper focuses on the presentation of an innovative fully automated electrophoresis system, currently being developed within the framework of a research project funded by the Greek National Programme for Competitiveness Entrepreneurship and Innovation. The system can process multiple protocols of gel electrophoresis, on a precast agarose film, utilizing a combination of hardware and software, with minimal intervention by humans. Healthcare professionals could significantly benefit from this system by obtaining fast and accurate results in a fully automated fashion, by eliminating human errors during the process.