Neonatal lung disease is often related to premature birth or congenital abnormalities. Structural MRI has been performed in these patients but does not indicate which lung regions perform gas exchange. Registered respiratory gated ultra-short echo-time proton MRI can produce lung ventilation maps in neonates throughout the respiratory cycle. This technique showed clear differences between a control subject and 2 patients with lung disease in terms of ventilation efficiency (inhaled air per milliliter of lung), spatial and temporal ventilation homogeneity. Further differences were shown post-surgical intervention, demonstrating the method and as a potential means to assess treatment efficacy.