Microcomputed tomography (Micro-CT) has the potential to noninvasively image the structure of organs in rodent models with high spatial resolution and relatively short image acquisition times. However, motion artifacts associated with the normal respiratory motion of the animal may arise when imaging the abdomen or thorax. To reduce these artifacts and the accompanying loss of spatial resolution, we propose a prospective respiratory gating technique for use with anaesthetized, free-breathing rodents. A custom-made bed with an embedded pressure chamber was connected to a pressure transducer. Anaesthetized animals were placed in the prone position on the bed with their abdomens located over the chamber. During inspiration, the motion of the diaphragm caused an increase in the chamber pressure, which was converted into a voltage signal by the transducer. An output voltage was used to trigger image acquisition at any desired time point in the respiratory cycle. Digital radiographic images were acquired of anaesthetized, free-breathing rats with a digital radiographic system to correlate the respiratory wave form with respiration-induced organ motion. The respiratory wave form was monitored and recorded simultaneously with the x-ray radiation pulses, and an imaging window was defined, beginning at end expiration. Phantom experiments were performed to verify that the respiratory gating apparatus was triggering the micro-CT system. Attached to the distensible phantom were 100 microm diameter copper wires and the measured full width at half maximum was used to assess differences in image quality between respiratory-gated and ungated imaging protocols. This experiment allowed us to quantify the improvement in the spatial resolution, and the reduction of motion artifacts caused by moving structures, in the images resulting from respiratory-gated image acquisitions. The measured wire diameters were 0.135 mm for the stationary phantom image, 0.137 mm for the image gated at end deflation, 0.213 mm for the image gated at peak inflation, and 0.406 mm for the ungated image. Micro-CT images of anaesthetized, free-breathing rats were acquired with a General Electric Healthcare eXplore RS in vivo micro-CT system. Images of the thorax were acquired using the respiratory cycle-based trigger for the respiratory-gated mode. Respiratory gated-images were acquired at inspiration and end expiration, during a period of minimal respiration-induced organ motion. Gated images were acquired with a nominal isotropic voxel spacing of 44 microm in 20-25 min (80 kVp, 113 mAs, 300 ms imaging window per projection). The equivalent ungated acquisitions were 11 min in length. We observed improved definition of the diaphragm boundary and increased conspicuity of small structures within the lungs in the gated images, when compared to the ungated acquisitions. In this work, we have characterized the externally monitored respiratory wave form of free-breathing, anaesthetized rats and correlated the respiration-induced organ motion to the respiratory cycle. We have shown that the respiratory pressure wave form is an excellent surrogate for the radiographic organ motion. This information facilitates the definition of an imaging window at any phase of the breathing cycle. This approach for prospectively gated micro-CT can provide high quality images of anaesthetized free-breathing rodents.