Respiratory sinus arrhythmia (RSA) is being used increasingly in psychophysiological studies as an index of vagal control of the heart and may be among the most selective noninvasive indices of parasympathetic control of cardiac functions. A comprehensive understanding of RSA, however, requires an appreciation of its multiple autonomic and physiological origins. We review the physiological bases of RSA and show that RSA arises from multiple tonic and phasic processes of both central and peripheral origin. These underlying mechanisms are at least partially differentiated, have distinct dynamics and consequences, and may be differentially sensitive to behavioral and cognitive events. These multiple mechanisms are relevant for psychophysiological studies of RSA, and a thorough understanding of RSA can only be achieved through an appreciation of the dynamics of its underlying origins. There is a distinction between the psychophysiological and neurophysiological domains, and conceptual and empirical bridges between these domains are needed.