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Photoacoustic (PA) tomography (PAT) breaks the barrier for high-resolution optical imaging in a strong light-scattering medium, having a great potential for both clinical implementation and small animal studies. However, many organs and tissues lack enough PA contrast or even hinder the propagation of PA waves. Therefore, it is challenging to interpret pure PAT images, especially three-dimensional (3D) PA images for deep tissues, without enough structural information. To overcome this limitation, in this study, we integrated PAT with X-ray computed tomography (CT) in a standalone system. PAT provides optical contrast and CT gives anatomical information. We performed agar, tissue phantom, and animal studies, and the results demonstrated that PAT/CT imaging systems can provide accurate spatial registration of important complementary contrasts.