Depressed patients may exhibit reduced heart rate variability (HRV), and antidepressants which block norepinephrine uptake may also lower HRV. This study compared paroxetine (PAR) and venlafaxine XR (VEN-XR) on HRV. Outpatients were randomly assigned to double-blind treatment with PAR up to 40 mg or VEN-XR up to 225 mg daily. HRV measures of parasympathetic control consisted of change in R-R interval during forced 10-second breaths and respiratory sinus arrhythmia (RSA) during paced breathing. Ex vivo estimates of serotonin and norepinephrine transporter occupancy were obtained before and after treatment, as were measures of depression, anxiety, and resilience. Plasma drug concentrations were measured at end point. Forty-nine patients entered treatment; 44 of whom were evaluable (n = 22 per group). Significant within-group reductions were noted in R-R interval variation and in RSA after VEN-XR only. Between-group analyses showed significant group-by-time interaction, with greater reduction in R-R interval variation and in RSA for VEN-XR compared with PAR. Improvement in resiliency correlated significantly with norepinephrine transporter occupancy for VEN-XR. Further comparisons of selective serotonin reuptake inhibitor and serotonin and norepinephrine reuptake inhibitor drugs on HRV are warranted.