Marine -3 polyunsaturated fatty acids (PUFA) may improve autonomic dysfunction, as indicated by an increase in heart rate variability (HRV) and reduce the risk of sudden cardiac death. Hence, the aim of this study was to investigate the effects of marine -3 PUFA on 24-h HRV in patients on chronic dialysis, who have a high risk of sudden cardiac death. Between June 2014 and March 2016, 112 patients on chronic dialysis from Denmark were allocated to a daily supplement of 2 g marine -3 PUFA or control for three months in a randomized, double-blinded, controlled trial. A 48-h Holter monitoring was performed and mean 24-h HRV indices for the two days were available in 85 patients. The mean age was 62.3 years (SD: 14.3) and median dialysis vintage was 1.7 years (IQR: 0.5, 6.4). Within-group and between-group changes in outcome were evaluated by a paired and two sample -test, respectively. Marine 3 PUFA did not change the primary endpoint SDNN (SD of all RR-intervals) reflecting overall HRV, but other HRV indices increased and the mean RR-interval increased significantly, corresponding to a decrease in heart rate by 2.5 beats per minute ( = 0.04). In conclusion, marine -3 PUFA did not change SDNN, but the mean heart rate was significantly reduced and changes in other HRV-indices were also observed, indicating an increase in vagal modulation that might be protective against malignant ventricular arrhythmias.