A cardiac catheterization procedure is a minimally-invasive surgery, which is employed in case of various cardiovascular conditions and requires a high precision. The method relies heavily on x-ray imaging and contrast dyes to guide the catheter inside the blood vessels, posing risks to patients and the medical staff. Thus, a miniaturized tri-axes magnetic sensor is developed for orientation monitoring using the Earth’s magnetic field, to assist the guiding of the catheter. The magnetic sensors are realized by flexible magnetic tunnel junctions on ultra-thin silicon substrate, ensuring a high sensitivity to magnetic fields. These flexible sensors have a bending endurance of over 1000 cycles without signs of fatigue. Three sensors are mounted on the tip of a catheter, implementing a sensor-on-tube concept for orthogonal 3-axes measurements. The sensors have an MR ratio of 29% and a high sensitivity of about 9 Ω/°. With a weight of only 16 μg and a thickness of 4 μm, each sensor adds a negligible weight and increase in size, making them attractive for applications, where extreme miniaturization is sought. The flexible tri-axes MTJ is mounted onto the tip of a cardiac catheter with 3 mm in diameter.