The factors influencing cleft repair are multiple and complex. A compromise must be achieved between facial growth, scarring, speech and language development, and psychological factors. However, one question remains unanswered. When is it safest in relation to the maturity of the respiratory control mechanisms? It was the aim of this pilot study to identify any problems with respiratory function after primary surgery. Of 39 patients, 42% were seen to have episodes of repeated hypoxemia of <92% saturation associated with bradycardia beyond 48 hours postoperatively. The implication of the findings and future directions for research are discussed.