The three-dimensional (3-D) X-ray crystal microscope is a new nondestructive tool for the 3-D characterization of the mesoscopic and nanoscopic materials structure. A prototype microscope is installed on beamline 34-ID at the advanced photon source and has begun initial operation. The prototype microscope has a routine spatial resolution of approximately 0.5 ϫ 0.5 ϫ 1 m 3 and can probe tens to hundreds of microns below a sample surface, depending on the composition of the sample. For each volume element measured, the microscope can determine between 10 and 16 parameters. The measured parameters are the local crystallographic phase (1 deg of freedom), the Eulerian angles of crystal orientation (3 deg of freedom), and the plastic and/or elastic strain-tensor elements (6 to 12 deg of freedom). The time required to collect each volume element varies between 1 and 14 seconds, depending on the precision of the parameters and the sample complexity. Much faster data acquisition and much better spatial resolution are certain in the near future. Some initial results are presented to illustrate how the 3-D X-ray crystal microscope can provide unprecedented information about the 3-D structure of materials.