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In the general population, reduced heart rate variability (HRV) has been associated with cardiovascular disease. However, its relation to chronic kidney disease (CKD) is debated. We therefore investigated the relation between low HRV and renal outcomes.In the population-based Prevention of REnal and Vascular ENdstage Disease study, renal outcomes (CKD, estimated glomerular filtration rate [eGFR], urinary albumin) were measured at baseline and three consecutive examinations. HRV measures (among which SDNN [standard deviation of normal-to-normal RR intervals]) were calculated from time series of beat-to-beat pulse wave recordings at baseline. The lowest (risk) quartile was compared with the upper three quartiles combined, in multivariable survival and linear mixed-effects analyses.In 4605 participants (49% males, age range = 33–80, 0.6% blacks), we observed 341 new participants of CKD during a median follow-up duration of 7.4 years. Low SDNN was associated with higher incidence of CKD (crude HR = 1.66, 95% CI = 1.30 to 2.12, p < .001), but this association was no longer significant after adjustment for age, sex, and cardiovascular risk factors (adjusted HR = 1.13, 95% CI = 0.86 to 1.48, p = .40, similar for other HRV measures). No associations between SDNN and eGFR trajectories were found in the total sample. However, in a subgroup of participants with baseline CKD (n = 939), we found a significant association of low SDNN (but not other HRV measures) with lower baseline eGFR, even after multivariable adjustment (adjusted βlevel difference = −3.73 ml/min/1.73 m2, 95% CI = −6.70 to −0.75, p = .014), but not with steeper eGFR decline.These results suggest that reduced HRV may be a complication of CKD rather than a causal factor.