-Previous investigations of the dynamic organization of the lower brainstem and its relation to peripheral and other central nervous sub-systems were predominantly performed by linear methods. These are based on time-averaging algorithms, which merely can be applied to stationary signal intervals. Thus the current concept of the common brainstem system (CBS) in the reticular formation (RF) of the lower brainstem and basic types of its functional organization have been developed. Here we present experiments where neuronal activities of the RF and the nucleus tractus solitarii (NTS, first relay station of baroreceptor afferents) were recorded together with related parameters of EEG, respiration, and cardiovascular system. The RF neurons are part of the CBS, which participates in regulation and coordination of cardiovascular, respiratory, and motor systems, and vigilance. The physiological time series thus acquired yield information about the internal dynamic coordination of the participating regulation processes. The major problem in evaluating these data is the non-linearity and instationarity of the signals. We used a set of especially designed time resolving methods to evaluate non-linear dynamic couplings in the interaction between CBS neurons and cardiovascular signals, respiration and the EEG, and between NTS neurons (influenced by baroreceptor afferents) and CBS neurons.