Cardiac and respiratory motion during the long acquisition times required in 3d magnetic resonance imaging (MRI) can lead to excessive image degradation and consequently poor diagnosis and interpretation in the thoracic region. This paper addresses the issue of obtaining good image quality with 3d gradient echo (GE) imaging in the study of the pulmonary vascular system and its diseases. To study the pulmonary vascular system two approaches have been considered. First, a proton density/inflow weighted scan consisting of a syncopated 3d FLASH acquisition is used to provide a 3d pulmonary angiogram. Secondly, aT 1 weighted scan using 3d IR-FLASH (inversion recovery FLASH) helps in determining the presence of pulmonary emboli. Multiple acquisitions and rectangular field of view are utilized to pseudogate to the respiratory period in order to reduce motion artifacts while keeping reasonable imaging times. Technical aspects on data collection during the approach to equilibrium and acquisition strategies in the presence of thoracic motion and its impact on vessel resolution are addressed. The method has proven successful for imaging volunteers and, more recently, in obtaining useful clinical information.