Micro-CT, a technique for imaging small objects at high resolution using micro focused x-rays, is becoming widely available for small animal imaging. With the growing number of mouse models of pulmonary pathology, there is great interest in following disease progression and evaluating the alteration in longitudinal studies. Along with the high resolution associated with micro CT comes increased scanning times, and hence minimization of motion artifacts is required. We propose a new technique for imaging mouse lungs in vivo by inducing an intermittent iso-pressure breath hold (IIBH) with a fixed level of positive airway pressure during image acquisition, to decrease motion artifacts and increase image resolution and quality. Mechanical ventilation of the respiratory system for such a setup consists of three phases, 1) tidal breathing (hyperventilated), 2) a breath hold during a fixed level of applied positive airway pressure, 3) periodic deep sighs. Image acquisition is triggered over the stable segment of the IIBH period. Comparison of images acquired from the same mouse lung using three imaging techniques (normal breathing / no gating, normal breathing with gating at End Inspiration (EI) and finally the IIBH technique) demonstrated substantial improvements in resolution and quality when using the IIBH gating. Using IIBH triggering the total image acquisition time increased from 15 minutes to 35 minutes, although total x-ray exposure time and hence animal dosage remains the same. This technique is an important step in providing high quality lung imaging of the mouse in vivo, and will provide a good foundation for future longitudinal studies.