To evaluate the complex time course of changes in respiratory sinus arrhythmia (RSA) during the menstrual cycle, daily beat-to-beat morning recordings of heart rate (HR) were carried out in 26 healthy female subjects (age 20-29 years) during two menstrual cycles. For determination of fast, vagally mediated variations of HR we used a robust time-domain measure of RSA (logRSA). We found pronounced changes in HR during the menstrual cycle with a minimum in the early follicular phase and a maximum in the late luteal phase. There were large differences between individuals in the fluctuations of logRSA during the menstrual cycle that were related to average HR: subjects with a low HR exhibited higher values of logRSA in the luteal compared to the follicular phase, whereas the trend was reversed in subjects with a high HR. The difference of extreme points of logRSA fluctuations (early follicular and mid luteal phase) was correlated to average HR (r=-0.64, P < 0.001). We conclude that different patterns of RSA fluctuations occur depending on the level of average HR.