We have investigated whether brainstem assessment using the Neuro Scope could be used for objective and quantitative monitoring of early development and later progress in Rett syndrome. Brainstem features can be seen on bedside examination of Rett patients and are included in the International Scoring system. The following cardiovascular vital signs were recorded simultaneously in real-time: cardiac vagal tone (CVT), cardiac sensitivity to baroreflex (CSB), heart rate (HR), and mean arterial blood pressure (MAP) and respiratory vital signs: breathing rate and pattern, transcutaneous partial pressures of oxygen (pO(2)) and carbon dioxide (pCO(2)). We assessed the occipito-frontal head circumference (OFHC), height and body mass index (BMI). Results are from 72 patients with classical Rett syndrome studied at the Swedish National Rett Centre. Three cardiorespiratory phenotypes, designated Forceful, Feeble and Apneustic breathers were present in similar proportions in the Rett population but early development measured by OFHC and BMI differed. Height was not affected. Baseline levels of CVT and CSB also differed within the phenotypes indicating differences in parasympathetic activities. However, parasympathetic activity in the whole population was similar to that previously reported in Rett. Baseline levels of MAP and HR were similar across the phenotypes, consistent with previous reports of little effect of Rett disorder on baseline sympathetic tone. Adverse responses to opiate analgesics and hypocapnoeic attacks were unique to specific phenotypes. We recommend early characterisation of these phenotypes in the management of Rett syndrome. We conclude that classical Rett syndrome consists of heterogeneous clinical phenotypes with distinct cardiorespiratory states. Brainstem functions can be used to identify these and to monitor development and treatment, thereby facilitating clinical management.