Partial left atrial ligation before cardiac septation redistributes intracardiac blood flow and produces left ventricular hypoplasia in the chick. We hypothesized that redistributed intracardiac blood flow adversely alters aortic arch development. We ligated the left atrial appendage with a 10-0 nylon suture at stage 21 chick embryos, then reincubated up to stage 34. Sham embryos had a suture tied adjacent to the atrial wall, and normal controls were unoperated. We measured simultaneous atrioventricular (AV) and dorsal aortic (DAo) blood velocities from stage 24 embryos with an ultrasound pulsed-Doppler flow meter; and the left and right third and fourth aortic arch blood flow with a laser-Doppler flow meter. Ventricular and atrial cross-sectional areas were measured from sequential video fields for planimetry. Intracardiac flow patterns were imaged on video by injecting India ink into the vitelline vein. In separate embryos, radiopaque microfil was injected into the cardiovascular system for micro-CT scanning. We analyzed the morphologic characteristics of the heart at stage 34. Active AV and DAo stroke volume (mm(3)), right third and fourth aortic arch blood flow (mm(3)/s) were all decreased in ligated embryos (P < 0.05) when compared with normal and sham embryos. Ventricular end-diastolic volume versus normal and sham embryos decreased by 45% and 46%, respectively (P < 0.05). India ink injection revealed altered right aortic arch flow patterns in the ligated embryos compared with normal embryos. micro-CT imaging confirmed altered arch morphogenesis. Alterations in intracardiac blood flow disrupt both early cardiac morphogenesis and aortic arch selection.