SummaryBackground and objectives Lower heart rate variability implies increased risk of cardiovascular disease. This study aimed to evaluate the relationship between mineral metabolism and heart rate variability and longitudinal changes of heart rate variability after parathyroidectomy in stage 5 CKD patients.Design, setting, participants, & measurements This cross-sectional study included 118 stage 5 CKD patients, 87 controls, and a prospective study in two subgroups classified as successful (n=17) and unsuccessful (n=4) parathyroidectomy follow-up enrolled from March of 2011 to December of 2012. Blood examination and 24-hour Holter for heart rate variability were measured.Results Most heart rate variability indices were lower in stage 5 CKD patients. In multivariate stepwise regression models, serum intact parathyroid hormone was correlated with mean normal-to-normal R-R intervals, mean heart rate, and very low frequency, serum calcium was correlated with SD of 5-minute average of normal R-R intervals, and serum phosphorus was correlated with very low frequency and low frequency/high frequency. Compared with baseline, the successful parathyroidectomy subgroup had significant improvements in mean normal-to-normal R-R intervals, mean heart rate, SD of normal-to-normal R-R intervals, SD of 5-minute average of normal R-R intervals, very low frequency, high frequency, and low frequency/high frequency. There was no significant change of heart rate variability in patients after unsuccessful parathyroidectomy.Conclusions Disorders of mineral metabolism are associated with decreased heart rate variability in stage 5 CKD. Successful parathyroidectomy may contribute to reverse this cardiovascular disease risk in severe secondary hyperparathyroidism patients.