Beamline P11 at PETRA III is dedicated to structural investigations of biological samples. It provides two experimental stations, one for macromolecular crystallography and one for X-ray microscopy. The microscope will provide full field Zernike phase contrast and scanning microscopy both in 2D and in tomographic mode. Full field microscopy with a field of view of 50 x 50 μm2 will allow to generate an overview of the sample and to select regions of interest for later inspection of the element distribution by X-ray fluorescence and diffraction in scanning mode. Central part of the microscope is an inhouse developed flexure based x,y,z scanner on top of a rotation stage. The scanner is operated in closed loop with piezo motors, has a travel range of 4 mm in horizontal and of 3 mm in vertical direction. With laser interferometers for closed loop operation a positioning accuracy of better than 5 nm is achieved in all directions. For precise sample rotation an in-vacuum air-bearing has been developed. An open bore in the center of the air-bearing allows cryogenic sample cooling by a cold He or N2 gas stream. Different optical elements such as beam defining pinholes, a condensor, zone plates, OSA, phase rings, etc. can be centered in the beam path by piezomotor driven x,y flexure elements mounted on a rail system which allows further positioning along the beam path. Different 2D detectors and two fluoresence detectors can be attached to the microscope.