Radiotherapy with carbon ion beams is a highly precise method for cancer treatment due to the finite range of the ions in matter, their low lateral scattering and an enhanced radiobiological effectiveness in the Bragg peak region. However, in tissue the carbon ions may undergo nuclear fragmentation, resulting in the production of lighter projectile fragments. Since the biological effect of the fragments differs from the primary particles, it is important to consider fragmentation in beam models used for therapy planning. Hybrid semiconductor pixel detectors enable the detection and tracking of single ions and are of great interest for ion beam therapy purposes in order to attend the needs of carbon ion beam therapy and further enhance its accuracy. Therefore, researchers of the Heidelberg University Hospital collaborate with ÚTEF ČVUT to carry out precise studies with the per-pixel energy sensitive Timepix device. Joint experiments are performed at the ion synchrotron at the Heidelberg Ion-Beam Therapy Center (HIT) in Germany, which is a hospital based facility for proton and carbon ion beam therapy. In the seminar, I will present a novel approach to measure the fragmentation of therapeutic carbon ion beams (E = 270 MeV/u) with the Timepix detector equipped with a 300 μm thick silicon sensor. Pattern recognition analysis of the detector signal shows a clear dependence of signal parameter distributions on tissue depth. This was used to identify the particular particle species in the spectra obtained behind PMMA plates of various thicknesses. In this way, discrimination between primary carbon ions and hydrogen, helium and heavier fragments is possible. The compact pixel detector was found to offer interesting spectroscopic capabilities while its size is much smaller than the devices used for ion spectroscopic measurements up to now (typically a few meters). Further on, the possibility of ion energy loss measurements on a single particle basis and non-invasive beam monitoring with Timepix detectors will be discussed.