A method for single photon counting transmission computed tomography (CT) is described. The method is based on an apparatus consisting of a radiation source and detectors on an opposite side of the subject from the source. The radiation source is for example an X-ray tube. The detectors are independently connected to parallel, fast, low-noise processing electronics capable of recording and counting individual X-ray photons at very high rate. In one embodiment of the invention, said detector is made of a scintillator coupled to a photodetector. The photodetector can be an avalanche photodiode (APD). The method comprises the steps of: directing the low energy radiation source toward the subject; detecting the radiation transmitted through the subject towards the detectors and recording the position and energy of each individual X-ray photon; rotating the radiation source and detectors around the subject; recording data for each position of the radiation source and detectors around the subject to form projections; and creating a CT image from the recorded projection data. The proposed method allows enhancing CT image contrast and reducing radiation dose to the patient by counting individual X-ray photons.