BACKGROUND: Heart rate variability (HRV) is known to be reduced in depression; however, is unclear whether this is a consequence of the disorder or due to antidepressant medication. METHODS: We analysed data on 4750 participants from the first wave of The Irish Longitudinal Study on Ageing (TILDA). Time [standard deviation of normal to normal intervals (SDNN ms2)] and frequency domain [low frequency (LF) and high frequency (HF)] measures of HRV were derived from 3-lead surface electrocardiogram records obtained during 10 min of supine rest. Depression was assessed using the Center for Epidemiologic Studies - Depression scale. RESULTS: Participants on antidepressants [with (n = 80) or without depression (n = 185)] differed significantly from controls (not depressed and not taking antidepressants n = 4107) on all measures of HRV. Depressed participants not taking antidepressants (n = 317) did not differ from controls on any measures of HRV. In linear regression analysis adjusted for relevant factors all antidepressants were associated with lower measures HRV. Participants on selective serotonin reuptake inhibitors (SSRIs) had higher measures of HRV relative to participants on tricyclic antidepressants or serotonin-norepinephrine reuptake inhibitors respectively. CONCLUSIONS: Our results suggest that reductions in HRV observed among depressed older adults are driven by the effects of antidepressant medications. SSRIs have less impact on HRV than other antidepressants but they are still associated with lower measures of HRV. Study limitations include the use of a self-report measure of depression and floor effects of age on HRV could have limited our ability to detect an association between HRV and depression.