The transition between sitting and standing represents a period of dynamic changes in cardiac autonomic control. Previous research using heart rate (HR) has suggested a biphasic HR response from sitting to standing with an initial increase in HR followed by an HR decrease before stabilizing at a level above the sitting level. These HR changes have been interpreted as mediated by sympathetic nervous system (SNS) activity. However, more direct measures of cardiac autonomic control have not been investigated in an active orthostasis paradigm. This is due in part to the requirement of stationarity for traditional spectral analytic techniques. In the present study, time-frequency analysis was used to assess the relative contributions of sympathetic and parasympathetic nervous system activity to the cardiac autonomic control during the transition of orthostasis. We examined the heart rate time series during the transition between sitting and standing, and the 60 s prior and the 60 s following the transition. The high frequency component of the HR spectra (an index of parasympathetic activity) decreased sharply at the point of transition and remained depressed relative to the low frequency component (an index of sympathetic activity). These results suggest that time-frequency analysis may be a useful technique to examine non-stationary time series. Furthermore, the transition of orthostasis may be mediated more via parasympathetic activity than by sympathetic activity.