X-ray computed tomography (CT) is widely used for non-invasive diagnostic imaging of the inside of the human body. It should be noted that the approximate effective radiation dose in a patient is 10 mSv. Under such an environment, X-ray photons are severely piled-up. Therefore, conventional CT only reconstructs energy integrated image, which may consist of beam hardening artifacts that have proven to be a problem. In contrast, photon counting CT (PC-CT) offers a low-dose multicolor CT imaging. The PC-CT also enables K-edge imaging that can improve the blood–tissue contrast using specific contrast agents. Moreover, the PC-CT has great advantages in (1) the simultaneous imaging of multiple contrast agents, and (2) the absolute quantification of contrast agents. Owing to these advantages, the PC-CT system can provide more detailed tissue diagnosis than conventional CT systems. Recently, we proposed a novel PC-CT system (Morita et al., 2017; Arimoto et al., 2017, Maruhashi et al., 2018) consisting of multipixel photon counter (MPPC) coupled with a high-speed scintillator, which is a cost-effective and easy to assemble system, as compared to other PC-CT devices based on cadmium zinc telluride. In this paper, we operated the K-edge imaging of specific contrast agents using a 16-channel MPPC PC-CT system. Our PC-CT system established appropriate energy thresholds and operated the simultaneous imaging of multiple contrast agents such as iodine and gadolinium. In addition, we estimated the absolute concentration of these contrast agents. The results show that our PC-CT system can provide more accurate diagnostic medical imaging, as compared to the conventional CT system.