In this work we used a novel CdTe photon counting x-ray detector capable of very high count rates to perform x-ray micro-computed tomography (microCT). The detector had 2 rows of 384 square pixels each 1 mm in size. Charge signals from individual photons were integrated with a shaping time of -60 ns and processed by an ASIC located in close proximity to the pixels. The ASIC had 5 energy thresholds with associated independent counters for each pixel. Due to the thresholding, it is possible to eliminate dark-current contributions to image noise. By subtracting counter outputs from adjacent thresholds, it is possible to obtain the number of x-ray photon counts in 5 adjacent energy windows. The detector is capable of readout times faster than 5 ms. A prototype bench-top specimen μCT scanner was assembled having distances from the tube to the object and detector of 11 cm and 82 cm, respectively. We used a conventional x-ray source to produce 80 kVp x-ray beams with tube currents up to 400 μA resulting in count rates on the order of 600 kcps per pixel at the detector. Both phantoms and a dead mouse were imaged using acquisition times of 1.8 s per view at 1° steps around the object. The count rate loss (CRL) characteristics of the detector were measured by varying the tube current and corrected for using a paralyzable model. Images were reconstructed using analytical fan-beam reconstruction. The reconstructed images showed good contrast and noise characteristics and those obtained from different energy windows demonstrated energy-dependent contrast, thus potentially allowing for material decomposition.