The respiration patterns of individuals with Rett syndrome are known to be dysrhythmic during wakefulness, suggesting cortical involvement of brainstem respiratory control. To investigate this involvement further, the waking breathing patterns of two girls with Rett syndrome were analysed during three phases: a quiet phase, and two phases during which visual and auditory stimuli were presented in controlled intervals. Differences were noted between the two subjects' respiratory patterns in both the quiet and stimulation phases. The usual quiet respiration patterns became more dysrhythmic for both girls during stimulation, with shortened breathing cycles and lengthened apnoeic pauses for the one subject, and increased numbers of apnoeic pauses and shallower breaths for the other. These results suggest that the cyclical brainstem control of breathing patterns in Rett syndrome may be subject to disruption as a result of cortical influences, including arousal subsequent to the engagement of attention.