Carbon ion beam radiotherapy enables a very localised dose deposition. However, even small changes in the patient geometry or positioning errors can significantly distort the dose distribution. A live, non-invasive monitoring system of the beam delivery within the patient is therefore highly desirable, and could improve patient treatment. We present a novel three-dimensional method for imaging the beam in the irradiated object, exploiting the measured tracks of single secondary ions emerging under irradiation.The secondary particle tracks are detected with a TimePix stack—a set of parallel pixelated semiconductor detectors. We developed a three-dimensional reconstruction algorithm based on maximum likelihood expectation maximization. We demonstrate the applicability of the new method in the irradiation of a cylindrical PMMA phantom of human head size with a carbon ion pencil beam of MeV u−1. The beam image in the phantom is reconstructed from a set of nine discrete detector positions between and from the beam axis. Furthermore, we demonstrate the potential to visualize inhomogeneities by irradiating a PMMA phantom with an air gap as well as bone and adipose tissue surrogate inserts.We successfully reconstructed a three-dimensional image of the treatment beam in the phantom from single secondary ion tracks. The beam image corresponds well to the beam direction and energy. In addition, cylindrical inhomogeneities with a diameter of cm and density differences down to g cm−3 to the surrounding material are clearly visualized.This novel three-dimensional method to image a therapeutic carbon ion beam in the irradiated object does not interfere with the treatment and requires knowledge only of single secondary ion tracks. Even with detectors with only a small angular coverage, the three-dimensional reconstruction of the fragmentation points presented in this work was found to be feasible.