Cardiac autonomic neuropathy (CAN) in diabetes has been called a "silent killer", because so few patients realize that they suffer from it, and yet its effect can be lethal. Early sub clinical detection of CAN and intervention are of prime importance for risk stratification in preventing sudden death due to silent myocardial infarction. This study presents the usefulness of heart rate variability (HRV) and complexity analyses from short term ECG recordings as a screening tool for CAN. Methods: A total of 17 sets of ECG recordings during supine rest were acquired from diabetic subjects with CAN (CAN+) and without CAN (CAN-) and analyzed. Poincaré plot indexes as well as traditional time and frequency, and the sample entropy (SampEn) measure were used for analyzing variability (short and long term) and complexity of HRV respectively. Results: Reduced (p > 0.05)_Poincaré plot patterns and lower (p < 0.05) SampEn values were found in CAN+ group, which could be a practical diagnostic and prognostic marker. Classification Trees methodology generated a simple decision tree for CAN+ prediction including SampEn and Poincaré plot indexes with a sensitivity reaching 100% and a specificity of 75% (percentage of agreement 88.24%). Conclusion: Our results demonstrate the potential utility of SampEn (a complexity based estimator) of HRV in identifying asymptomatic CAN.