Automated high-throughput characterization is an essential enabling technology for autonomous materials research. Traditional microstructural characterization techniques, particularly those that require careful surface preparation, are difficult to adapt to a high-throughput environment. In contrast, transmission x-ray diffraction (XRD) provides the ability to probe bulk microstructure with minimal sample preparation. We have designed and constructed a new instrument for high-energy transmission XRD and integrated it into the Artificial Intelligence for Materials Design (AIMD) automated laboratory at Johns Hopkins University. The new instrument combines a high-brightness, high-energy x-ray beam with a low-noise, high-sensitivity x-ray detector and robotic sample handling. This combination enables autonomous data collection and analysis for high-throughput characterization of crystalline phases, texture, grain size, and chemical composition (by x-ray fluorescence spectroscopy performed simultaneously with XRD). In this talk we describe the instrument design and data analysis (via point-to-point comparison of regions on samples using similarity metrics) for high-throughput characterization. Examples are drawn from commercial structural aluminum alloys, refractory high-entropy alloys, and complex concentrated ceramics.