We investigated the electrocardiographic substrate underlying the asymmetry of Poincaré plots of NN intervals (NNI) on different time scales and conceived a method for automatic asymmetry quantification (AQUA), which is based on the observation that left-sided comet asymmetry (A(L)) is due to sudden increases (SIC), and right-sided comet asymmetry (A(R)) to sudden decreases (SDC) of cycle lengths, and that both the SIC and SDC episodes were consistently associated with significant changes in P-wave magnitude and/or polarity indicating a shift in dominant pacemaker activity. The performance of AQUA was validated in 15 endurance trained athletes (age: 29 +/- 6 years) exhibiting marked comet asymmetry, and 11 untrained controls (age: 40 +/- 15 years) with symmetrical comet patterns. SICs were reliably identified by AQUA with a sensitivity of 0.950 and a specificity of 0.985, and SDCs with a sensitivity of 0.952 and a specificity of 0.965. In the athletes, the magnitude of SICs exceeded that of SDCs significantly, and the occurrence of SICs and SDCs was closely correlated with periods of increased efferent vagal activity. It is concluded that AQUA is a useful tool for the identification and quantification of specific aspects of nonlinear heart rate dynamics manifesting as Poincaré plot asymmetries.