The use of robotic instruments capable of assisting medical staff during interventional or diagnostic procedures is growing rapidly today. Recently, a robotic system (Niobe, Stereotaxis Inc., USA) has been developed for navigating magnetically enabled tools inside the human body by controlling a magnetic field. This paper reports the fundamentals of this technology and reviews its application in two specific medical fields, cardiology and gastroenterology, in which its uses are different and are at dissimilar stages of development. In the first case, the system is already approved and employed for clinical treatments, such as magnetic steering of endocardial catheters for atrial fibrillation ablation, which is specifically considered in this article. In the second case, initial investigations are being performed today to study the potential magnetic maneuverability of ingestible video capsules adopted for endoscopic explorations of the digestive tract. This paper reviews current achievements and highlights future challenges related to each of these applications.