A transportation system for paraffin embedded tissues includes a placing assembly, a bearing unit and a storage device. The placing assembly includes a horizontal moving assembly, a vertical moving assembly, a rotation assembly and a placing unit. The horizontal and vertical moving assemblies move the placing unit in horizontal and vertical directions, respectively, and the rotation assembly allows the placing unit to rotate around a vertical axis. The bearing unit receives the paraffin embedded tissues. The storage device has a rotation plate including a plurality of receiving slots each for storing the bearing unit. The placing unit is configured to remove the bearing unit from the storage device, move the bearing unit to a processing apparatus located at another side of the placing assembly, remove the bearing unit from the processing apparatus, and transport the bearing unit to the receiving slot of the storage device.