Abstract: Both CT and MRI are the most widely used clinical imaging facilities nowadays. This article is invited to give a significant and valuable comparison between CT and MRI in many aspects, such as imaging principles, performances, demand, features, parameters, sensibilities, securities, nature of signals, signals standards, theories of reconstruction methods, etc. It also traces back to the history resemblance of these two methods, and expounds that the sole development of these two mathematical methods (Radon Transform & Fourier Transform) roots in the distinct difference between CT and MR signals. Signal of MR is in time domain and signal of X-ray is in space domain. It is also pointed out that the mathematical foundation of PET, SPECT, OCT, UCT are of the same clan, except the MRI.