Heart rate variability and baroreflex sensitivity are two readily accessible methods available to assess control of heart rate by the autonomic nervous system. Heart rate variability can provide information regarding neural (parasympathetic, sympathetic, reflex) and nonneural (hormones, thermoregulation) control of heart rate. Baroreflex sensitivity provides information on how effective the autonomic nervous system is in rapidly changing heart rate in response to changes in blood pressure. Methods are presented on how to calculate heart rate variability using frequency domain analysis and how to calculate baroreflex sensitivity using the sequence method and α-coefficient method of analysis. Data is presented from a variety of rat strains (control, hypertensive, kidney disease, depressed) to indicate the utility of these methods for comparing autonomic regulation of the heart in both anaesthetised animals via intra-arterial recordings and conscious animals using telemetry.