INTRODUCTION: This pilot study assessed the association between critical illness polyneuropathy (CIP) and decreased heart rate variability (HRV) in intensive care patients. METHODS: All patients admitted to the intensive care unit and expected to be ventilated for at least 72 hours were included and underwent weekly electromyograms and HRV analyses for three weeks. HRV was assessed by time domain analysis of 24h recording electrocardiograms, and alterations in HRV were assessed as the square root of the mean squared differences of successive RR intervals (RMSSD) </= 15. RESULTS: We evaluated 26 patients, 12 men and 14 women, median age 64 years. During follow-up, 12 patients died and 9 developed CIP. CIP was not associated with age, sex, simplified acute physiology score II and treatment agents. Altered RMSSD tended to be associated with onset of CIP (P=0.06). Altered RMSSD occurred earlier or at the same time as electromyogram abnormalities in all CIP patients, but the difference was not significant. CONCLUSION: Altered HRV, may be associated with the onset of CIP in ICU patients. Although not statistically significant (P=0.06), altered RMSSD may be a surrogate marker of CIP in ICU patients undergoing mechanical ventilation. The physiological pathway linking HRV and CIP remains uncertain.