BACKGROUND: Non-linear heart rate variability (HRV) indices were hypothesized to correlate with cardiac function, fluid overload and physical performance in hemodialysis patients. METHODS: Twenty-four-hour Holter electrocardiograms were recorded in patients enrolled in the Frequent Hemodialysis Network (FHN) Daily Dialysis Trial. Correlations between non-linear HRV indices and left ventricular ejection fraction (LVEF), left ventricular end-diastolic volume (LVEDV), extracellular volume (ECV)/total body water (TBW) ratio, the SF-36 Physical Health Composite (PHC) and Physical Functioning (PF) scores were tested. RESULTS: We studied 210 subjects (average age 49.8 +/- 13.5 years, 62% men, 42% diabetics). In non-diabetic patients, multiscale entropy (MSE) slope sample entropy (SampEn) and approximate entropy (ApEn) correlated positively with LVEF, PF and PHC and inversely with LVEDV and ECV/TBW. Spectral power slope correlated positively with ECV/TBW (r = 0.27). Irregularity measures (MSE ApEn and MSE SampEn) correlated positively with LVEDV (r = 0.19 and 0.20). CONCLUSION: Non-linear HRV indices indicated an association between a deteriorated heart rate regulatory system and impaired cardiac function, fluid accumulation and poor physical condition.