Abstract An X-ray micro-radiographic system based on the Medipix2 semiconductor pixel detector for dynamic high spatial resolution and for high contrast imaging has been developed. Our system is based on a micro-focus and nano-focus X-ray tube and the hybrid single-photon counting silicon pixel detector Medipix2 (matrix 256×256 sq. pixels of 55 μm pitch). This compact table-top system stands promising as a new tool in the field of small animal imaging as well as in the in-vivo observation of dynamic processes inside living organisms. The main advantages of these Medipix2 pixel detectors include: high sensitivity to low-energy X-ray photons; position sensitive and noiseless single-photon detection with preselected photon energies; single-quantum counting in each pixel performed by digital counter (therefore there is no dark current); digital integration (providing unlimited dynamic range and absolute linearity in device response to number of photons, high sensitivity and high contrast); real-time digital information, high-speed digital communication and data transfer. We improve the picture quality with the help of statistical data analysis and extended the calibration of individual pixels response. 2D and 3D radiographic images of samples demonstrate the potential and applicability of our system for precise in-vivo X-ray high-resolution dynamic diagnostic and biological studies. Obtained results are shown on small animal and organic samples.