An X-ray diffraction apparatus provides analysis in either transmission or reflective mode and easy conversion between the two modes. An X-ray source and X-ray detector are each connected to a different circle of a goniometer. The two circles may be rotated independently to position the source and detector on the same side of a sample library for reflection mode operation, or on opposite sides of the sample library for transmission mode operation. The sample library has a horizontal orientation that allows open sample containers of the library to maintain the sample without spillage, and it connects to an XYZ stage that can move in three dimensions. The system may use a beamstop, and the goniometer and XYZ stage be motorized and controlled for automated sample analysis.