The high spatial and temporal resolution demands for imaging physiological function in the rodent call for the use of novel ways to combine information from different imaging modalities. This work describes ventilation imaging using hyperpolarized (HP) 3He magnetic resonance imaging (MRI) and perfusion imaging using X-ray digital subtraction angiography (DSA). We illustrate the key steps needed to combine the complementary data from the two modalities to provide qualitative and quantitative information on gas exchange in the lungs. The results indicate that multimodality imaging of pulmonary function in small animals can provide functional information at higher spatial and temporal resolution compared to many traditional imaging techniques. © 2006 IEEE.