Transient systolic murmurs in neonates and premature infants due to mild left (LPA) and right (RPA) pulmonary branch stenosis is recognized but follow up studies are lacking. We studied echocardiographically 21 neonates with murmur and 10 controls. Diameters of the main pulmonary artery (MPA), LPA and RPA were smaller in patients with murmur. Colour-coded Doppler showed turbulent flow in LPA and RPA in 20/21 (95%) patients and flow velocities of both pulmonary branches were significantly higher than in controls. The follow up study at 3 months in 14/21 (67%) patients showed absent or decreased murmur in 9 (64%). Echographically, absolute and relative diameters of LPA and RPA increased whereas the ratio of MPA/aorta did not change suggesting accelerated growth or dilatation of the pulmonary branches. Flow velocities decreased significantly in the branches. Thus, transient systolic murmurs in neonates are associated with temporary relative hypoplasia of the pulmonary branches which showed increased growth leading to disappearance of the murmur in most cases within 3 months of life.