Infants with surgically correctable anomalies, abdominal wall defects (AWD) or congenital diaphragmatic hernia (CDH) may have poor postnatal diaphragmatic function, because the low intra-abdominal pressure experienced by such patients in utero could result in impaired diaphragmatic development. Our objective was to compare postoperative diaphragmatic function of infants with CDH or AWD to that of gestational age-matched controls. Diaphragmatic function was assessed by measurement of the transdiaphragmatic pressure and maximum inspiratory pressure at the mouth generated during crying against an occlusion. In addition, the transdiaphragmatic pressure produced by unilateral and/or bilateral magnetic stimulation of the phrenic nerves (TwPdi) was examined. Lung volume was assessed by measurement of functional residual capacity (FRC) using a helium gas dilution technique. Ten infants with CDH, 26 with AWD infants (19 gastroschisis, seven exomphalos), and 36 gestational age-matched controls were studied. Compared with their matched controls, the eight CDH infants with left-sided defects had significantly lower left (p < 0.01) and right (p < 0.05) TwPdi and FRC (p < 0.01), and the gastroschisis infants, but not those with exomphalos, had significantly lower left and right TwPdi (p < 0.05). There were no significant differences in transdiaphragmatic pressure and maximum inspiratory pressure at the mouth between the CDH or AWD infants and the controls. Diaphragmatic function postoperatively is impaired in infants with CDH or gastroschisis.