Neonatal exposure to intermittent hypoxia results in altered ventilatory response to subsequent hypoxia in animal models. The effect of similar exposure in human infants is unknown. Our objective was to determine the impact of sleep disordered breathing (SDB) in early infancy on ventilatory response in infants. We recruited consecutive infants with cleft lip and/or palate (CL/P) to undergo ventilatory response testing using exposure to a hypoxic (15% O2) gas mixture during sleep. This population is at high risk of SDB because of smaller airway caliber and abnormal palatal muscle attachments predisposing them to airway obstruction of ranging severity from birth. Ventilatory responses were compared between infants with a low apnea–hypopnea index (AHI; AHI < 15 events/hr) and a high AHI (AHI ≥ 15 events/hr). Testing was successfully completed in 22 of 23 infants who underwent testing at 4.4 ± 4.8 months. Infants with high AHI had lower weight z-scores, higher number of oxygen desaturation events during sleep, but similar oxygen saturation (SpO2) nadir compared to infants with low AHI. The pattern of ventilatory response to hypoxia differed between the two groups; infants with high AHI had an earlier ventilatory decline and a blunted maximal ventilatory response to hypoxia. Infants with a high AHI use a different strategy to augment ventilation in response to hypoxia; while infants with a low AHI initially increased respiratory rate, tidal volume was the first parameter to increase in infants with high AHI. These results demonstrate that SDB in infancy is associated with altered ventilatory response to hypoxia.