Heterotaxy (HTX) congenital heart disease (CHD) patients with ciliary dysfunction (CD) have been shown to have increased postoperative respiratory morbidity. We hypothesized that non-HTX CHD infants with CD also will have increased postoperative morbidity, particularly respiratory complications. Sixty-three infants with non-HTX CHD undergoing cardiac surgery were enrolled. Tests commonly used to assess for CD, nasal nitric oxide (nNO) measurements and nasal epithelial ciliary motion (CM) assessment, were obtained. Baseline characteristics and postoperative outcomes were collected and analyzed. Non-HTX CHD infants exhibited a high prevalence of abnormal CM (32%) and low nNO (39%). This finding was not correlated with demographics or surgical complexity. Infants with abnormal CM had increased odds of requiring noninvasive positive pressure ventilation (odds ratio [OR], 6.5; 95% confidence interval [CI], 1.5-29.4; P = .016) and respiratory medication use (OR, 4.4; 95% CI, 1.5-13.3; P = .01). In contrast, infants with low nNO showed evidence of abnormal pre- and postoperative systolic function (40% vs 4%; P = .004, and 34% vs 13%; P = .056, respectively) and had greater odds of acquiring infections (OR, 4.9; 95% CI, 1.4-17; P = .014). Non-HTX CHD infants with abnormal CM showed increased postoperative morbidity associated with poor respiratory outcomes. In contrast, low nNO correlated with reduced hemodynamic function. These findings suggest screening for abnormal CM may allow perioperative interventions to reduce pulmonary morbidities. Whether low nNO may prognosticate poor hemodynamic function warrants further investigation.