To elucidate the origin of transient heart murmur during the late neonatal period, we examined 50 neonates with this type of heart murmur and compared them with 50 controls. We serially examined the morphology of and blood flow in the main pulmonary artery (MPA), the right pulmonary artery (RPA), and the left pulmonary arteries (LPA) using two-dimensional and Doppler echocardiography. The heart murmurs were first noticed at 6 to 60 days after birth (mean 33 +/- 14). At that time, the diameters of both the RPA and the LPA in the heart murmur group were significantly smaller than those in the control group, and the velocities of blood flow in the right and left pulmonary arteries in the heart murmur group were significantly greater than those in the control group. When the heart murmur disappeared, the diameters and the flow velocities of both the RPA and the LPA were not different compared with the control group. Two cases in the heart murmur group continued to have a heart murmur and were diagnosed as having intrinsic congenital peripheral pulmonary artery stenosis. In conclusion, our findings suggest that a transient heart murmur in the late neonatal period is caused by transient branch pulmonary arteries stenosis during the transitional circulation from fetus to neonates.