Research on pathological calcifications constitutes an exciting topic at the interface between physics, chemistry and medicine. The relationship between their physicochemical characteristics and the pathology responsible for their formation offers a unique opportunity to perform a significant medical diagnosis, to assess the interaction between drugs and these biological entities as well as to develop new drugs. Regarding synchrotron radiation, the emergence of microbeam allows the clinician to perform an early diagnosis. Indeed, we will start this review with a clinical case where Fourier transform infrared spectroscopy using synchrotron radiation as a probe allowed the clinician to save the kidney function of a patient. Following this example, we will see that investigations on pathological calcifications constitute an elegant way to gather major information on different public health problems such type 2 diabetes as well as on rare diseases. To attain this goal, this mini-review dedicated to structural and chemical investigations and based on selected and recent data collected through techniques using third generation synchrotron radiation as a probe is proposed to the reader.