Purpose To evaluate the use of gallium-68 ( 68 Ga) macroaggregated albumin (MAA) positron emission tomography/computed tomography (PET/CT) perfusion imaging combined with Technegas single-photon emission computed tomography/computed tomography (SPECT/CT) ventilation imaging in rabbits with experimental pulmonary emboli (PE). Methods Technegas SPECT/CT ventilation and a 68 Ga-MAA PET/CT perfusion scan (V/Q scan) were performed in 12 rabbits before and one hour after artificial induction of PE. Technegas SPECT/CT and 68 Ga-MAA PET/CT images were evaluated by a nuclear medicine physician who recorded the presence, number, and location of PE on a per-lobe basis. The sensitivity, specificity, and accuracy of Technegas SPECT/CT and 68 Ga-MAA PET/CT for detecting PE were calculated using a histopathological evaluation as a reference standard. Results A total of 60 lung lobes were evaluated in 12 rabbits, and PE was detected in 20 lobes in V/Q scans and histopathological analysis. The overall sensitivity, specificity and accuracy were 100%, 100%, and 100%, respectively, for both the Technegas SPECT/CT and 68 Ga-MAA PET/CT V/Q scans. Conclusion Technegas/ 68 Ga-MAA V/Q scans have good sensitivity, specificity and accuracy in the detection of PE in this animal model study.