In newborn infants, thoraco-abdominal surgery is a serious intervention with respect to gas exchange and lung mechanics. This prospective clinical study compared surgery-induced changes in functional residual capacity (FRC) and ventilation inhomogeneity (VI) indices with changes in conventional monitoring parameters. Of 29 ventilated newborns (mean weight 2,770+/-864 g at surgery), 13, nine and seven underwent thoracic, abdominal or congenital diaphragmatic hernia (CDH) surgery, respectively. The multiple breath washout (MBWO) technique using heptafluoropropane as tracer gas (Babylog 8000; Dräger, Lübeck, Germany) was performed <6 h before surgery, 22-24 h after surgery and <6 h before extubation. Gas exchange, respiratory mechanics, FRC and VI index data were recorded. Thoraco-abdominal surgery resulted in changes to FRC and VI indices in a procedure-specific manner; however, these changes were not reflected in conventional mechanical or ventilatory monitoring parameters. FRC decreased in non-CDH infants, while FRC increased and VI indices decreased in CDH infants. Despite improvements, the differences in FRC and VI between CDH and non-CDH infants indicated persistent impaired lung function in CHD infants. MBWO can be advantageously used to measure the effect of surgery on the lung. While FRC and VI indices changed following surgery, conventional monitoring parameters did not.