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To verify the influence of different volumes and intensities of aerobic exercise on cardiac autonomic function (CAF) through heart rate variability (HRV) analysis as well the influence of β2 adrenergic receptor (ADRB2) variants in overweight/obese individuals.70 physically inactive adults were randomly allocated into the following 16-week training: 1-high-intensity interval training (HIIT) (n = 25, 1 × 4 min bout at 85-95%HR peak, 3×/week), 4-HIIT (n = 26, 4 × 4 min bouts at 85-95%HR peak, interspersed with 3 min of recovery at 50-70%HR peak, 3×/week), and moderate continuous training (MCT) (n = 19, 30 min at 60-70%HR peak, 5×/week). Before and after the exercise training, anthropometric, BP, cardiorespiratory fitness, and HRV measures were evaluated. R-R intervals recorded for 10 min in a supine position at pre- and post-intervention were used to analyze HRV in the plot-Poincare indexes (SD1, SD2), and frequency-domain (LF, HF, LF/HF). Full blood samples were used for genotyping.4-HIIT and MCT showed positive outcomes for almost all variables while 1-HIIT had a positive influence only on SBP and SD2 index. No associations were observed between isolated ADRB2 variants and changes in HRV. In the analysis of the interaction genotypes, all groups responded positively for the SD1 index of HRV and only the H1 (GG and CC) and H2 (GG and CG + GG) groups presented increases in the RMSSD index. Furthermore, there was an increase in the LF index only in the H3 (CC and AA + AG) and H4 (AA + AG and CG + GG) groups.ADRB2 variants and aerobic exercise training are important interacting variables to improve autonomic function and other health variables outcomes in overweight or obese individuals.