We studied heart rate variability in rats by power scaling spectral analysis (PSSA), autoregressive modeling (AR), and detrended fluctuation analysis (DFA), assessed stability by coefficient of variation between consecutive 6-h epochs, and then compared cross-correlation among techniques. These same parameters were checked from baseline conditions through acute and chronic disease states (streptozotocin-induced diabetes) followed by therapeutic intervention (insulin). Cross-correlation between methods over the entire time period was r = 0.94 (DFA and PSSA), r = 0.81 (DFA and AR), and r = 0.77 (AR and PSSA). Under baseline conditions the scaling parameter measured by DFA and PSSA and the high-frequency (HF) component measured by AR fluctuated around an average value, but these fluctuations were different for the three methods. After diabetes induction, a strong correlation was found between the HF power and the short-term scaling parameter. Despite their differences in methodology, DFA and PSSA assess changes in parasympathetic tone as detected by autoregressive modeling.