Microfluidics is assumed to be one of the leading and most promising areas of research since the early 1990s. In microfluidic systems, small spherical magnetic particles with superparamagnetic properties, called magnetic beads, play an important role in the design of innovative methods and tools, especially in bioanalysis and medical sciences. The intention of this review paper is to address main aspects from the state-of-the-art in the area of magnetic bead research, while demonstrating the broad variety of applications and the huge potential to solve fundamental biological and medical problems in the fields of diagnostics and therapy. Basic issues and demands related to the fabrication of magnetic particles and physical properties of nanosize magnets are discussed in Section 2. Of main interest are the control and adjustment of the nanoparticles’ properties and the availability of adequate approaches for particle detection via their magnetic field. Section 3 presents an overview of magnetic bead applications in nanomedicine. In Section 4, practical aspects of sample manipulation and separation employing magnetic beads are described. Finally, the benefits related to the use of magnetic bead-based microfluidic systems are summarized, illustrating ongoing questions and open tasks to be solved on the way to an approaching microfluidic age.