Purpose: Carbon nanotube ͑CNT͒ based field emission x-ray source technology has recently been investigated for diagnostic imaging applications because of its attractive characteristics including electronic programmability, fast switching, distributed source, and multiplexing. The purpose of this article is to demonstrate the potential of this technology for high-resolution prospective-gated cardiac micro-CT imaging. Methods: A dynamic cone-beam micro-CT scanner was constructed using a rotating gantry, a stationary mouse bed, a flat-panel detector, and a sealed CNT based microfocus x-ray source. The compact single-beam CNT x-ray source was operated at 50 KVp and 2 mA anode current with 100 m ϫ 100 m effective focal spot size. Using an intravenously administered iodinated bloodpool contrast agent, prospective cardiac and respiratory-gated micro-CT images of beating mouse hearts were obtained from ten anesthetized free-breathing mice in their natural position. Fourdimensional cardiac images were also obtained by gating the image acquisition to different phases in the cardiac cycle. Results: High-resolution CT images of beating mouse hearts were obtained at 15 ms temporal resolution and 6.2 lp/mm spatial resolution at 10% of system MTF. The images were reconstructed at 76 m isotropic voxel size. The data acquisition time for two cardiac phases was 44Ϯ 9 min. The CT values observed within the ventricles and the ventricle wall were 455Ϯ 49 and 120Ϯ 48 HU, respectively. The entrance dose for the acquisition of a single phase of the cardiac cycle was 0.10 Gy. Conclusions: A high-resolution dynamic micro-CT scanner was developed from a compact CNT microfocus x-ray source and its feasibility for prospective-gated cardiac micro-CT imaging of free-breathing mice under their natural position was demonstrated.