BACKGROUND: Several methods have been used to assess cardiac vagal modulation, but there are gaps regarding the association and accuracy of these methods. OBJECTIVE: To investigate the association between three valid, reproducible and commonly methods used to assess cardiac vagal modulation and compare their accuracies. METHODS: Thirty healthy men (23 +/- 4 years) and 15 men with coronary artery disease (61 +/- 10 years) were evaluated in counterbalanced design by Heart Rate Variability (HRV; variables: the time domain = pNN50, SDNN and RMSSD, the frequency domain HF = ms(2) and HF n.u.), Respiratory Sinus Arrhythmia (RSA) and 4-second Exercise Test (T4s). Thirty healthy men (23 +/- 4 years) and 15 men with coronary artery disease (61 +/- 10 years) were evaluated in counterbalanced order by Heart Rate Variability (HRV; variables: the time domain = pNN50, SDNN and RMSSD, the frequency domain HF = ms(2) and HF n.u.), Respiratory Sinus Arrhythmia (RSA) and 4-second Exercise Test (T4s). RESULTS: Healthy subjects had higher vagal modulation by the three methods (p <0.05). There was a correlation in the healthy group (p <0.05) between the results of HRV (SDNN and pNN50 and RSA, but there was no correlation between the T4s and the other two methods. In the group with coronary artery disease, there was a correlation between the results of HRV (pNN50, SDNN, RMSSD, HF ms(2) and HF n.u.) and RSA. In addition, there was a correlation between the RSA and T4s. Finally, the T4s and RSA methods presented more accurate effect size and better accuracy (p <0.05), when compared to the HRV. CONCLUSION: HRV and RSA generated partially redundant results in healthy subjects and in patients with coronary artery disease, while the T4s generated results that were complementary to HRV and RSA in healthy subjects. In addition, RSA and T4s methods were more accurate when discriminating cardiac vagal modulation between healthy subjects and patients with coronary artery disease, when compared to HRV.