Microsystems combining fluid dynamics and electric-field-induced forces have emerged as powerful tools for manipulating and isolating biological species. Advances in electrokinetic theory, combined with optimized microfabrication processes, are at the core of the development of high-throughput devices capable of directly handling unprocessed samples and seamlessly integrating analytical functions. Electrokinetic technologies can manipulate bioparticles ranging from a few nanometres to tens of micrometres, achieving throughputs of up to 106 particles per second, comparable to other state-of-the-art techniques. This Review starts by presenting the fundamentals of physical phenomena underlying the generation of electrokinetic forces applied to biological particles. We then provide an overview of existing technologies, with a focus on key factors influencing the development of new electrokinetic microdevices. Lastly, we delve into the unique challenges associated with translating these integrated microsystems into commercial systems, and we highlight the opportunities, future research directions and applications in the fields of in vitro diagnostics and healthcare.