BACKGROUND Altered pattern of respiration has been shown to affect both the cardiac as well as cortical activity, which is the basis of central-autonomic dual interaction concept. On the other hand, effect of this association between altered breathing with slow cortical activity, that is, electroencephalography (EEG) theta waves (associated with learning and relaxed alertness) on the cardiac autonomic balance is largely unclear. OBJECTIVE The study aims to understand this interaction in response to altered respiratory patterns, for example, voluntary apnea, bradypnea, and tachypnea in terms of EEG and heart rate variability (HRV) correlates in normal healthy subjects. METHODS This study was conducted on 32 adult male subjects. EEG from F3, F4, P3, P4, O1 and O2 cortical areas and Lead II electrocardiography for HRV analysis was continuously recorded during aforesaid respiratory interventions. Power spectral analysis of EEG for theta waves and HRV measures, that is, RMSSD, pNN50, HF, LF, and LF/HF was calculated as % change taking resting value as 100%. RESULTS Apnea caused decrease in theta power, whereas an increase in LF/HF was observed in HRV. Bradypnea on the other hand, did not elicit any significant change in power of theta waves. However, decreased RMSSD and pNN50 were observed in HRV. Tachypnea led to increase in theta power with HRV depicting significantly decreased RMSSD and pNN50. Besides, significant correlation between EEG and HRV measures was found during tachypnea, which shifted toward posterior cortical sites as compared to resting condition. CONCLUSIONS Various altered respiratory patterns caused either depressed parasympathetic or increased sympathetic output, whereas increased theta power along with posterior shift of correlation between theta power and HRV measures observed during post tachypnea might be due to involvement of global brain areas due to respiration-coupled neuronal activity. Thus, a definite link between cortical activity and autonomic output in relation to altered respiratory patterns may be suggested.