Rearranged origin of heart rhythm in patients with atrial fibrillation (AF) influences the regulation of the heart and consequently the respiratory rhythm, and the bidirectional interaction of these rhythms not documented. Hence, we examined coupling of the RR interval and the respiration (Resp) signal by coherence, Granger causality and the cross-sample entropy method of time series analysis in patients with AF and a healthy control group. In healthy subjects, the influence of respiration on cardiac rhythm was found as increased coherence at the breathing frequency (BF) range, significantly stronger interaction and synchrony from Resp to RR than from RR to Resp. On the contrary, in patients with AF, coherence at BF diminished, there were no causal interactions between signals in both directions, which resulted in equally great asynchrony between them. In AF, the absence of full functionality of the sinoatrial node, as an integrator of neural cardiac control, resulted in diminished vagal modulation of heart periods and consequently impaired bidirectional cardio-respiratory interaction.