Scanning and transmission electron microscopy, synchrotron X-ray diffraction, microtomography and ultrasonic velocity measurements were used to characterize microstructures and anisotropy of three deeply buried Qusaiba shales from the Rub’al-Khali basin, Saudi Arabia. Kaolinite, illite-smectite, illite-mica and chlorite show strong preferred orientation with (001) pole figure maxima perpendicular to the bedding plane ranging from 2.4–6.8 multiples of a random distribution (m.r.d.). Quartz, feldspars and pyrite crystals have a random orientation distribution. Elastic properties of the polyphase aggregate are calculated by averaging the single crystal elastic properties over the orientation distribution, assuming a nonporous material. The average calculated bulk P-wave velocities are 6.2 km/s (maximum) and 5.5 km/s (minimum), resulting in a P-wave anisotropy of 12%. The calculated velocities are compared with those determined from ultrasonic velocity measurements on a similar sample. In the ultrasonic experiment, which measures the effects of the shale matrix as well as the effects of porosity, velocities are smaller (P-wave maximum 5.3 km/s and minimum 4.1 km/s). The difference between calculated and measured velocities is attributed to the effects of anisotropic pore structure and to microfractures present in the sample, which have not been taken into account in the matrix averaging.