There is only very limited data examining cardiovascular responses in real-world endurance training/competition. The present study examines the influence of a marathon race on non-linear dynamics of heart rate (HR) variability (HRV). Eleven male recreational runners performed a self-paced marathon road race on an almost flat profile. During the race, heart rate and beat-to-beat (RR) intervals were recorded continuously. Besides HRV time-domain measurements, fractal correlation properties using short-term scaling exponent alpha1 of Detrended Fluctuation Analysis (DFA-alpha1) were calculated. The mean finishing time was 3:10:22 ± 0:17:56 h:min:s with a blood lactate concentration of 4.04 ± 1.12 mmol/L at the end of the race. Comparing the beginning to the end segment of the marathon race (Begin vs. End) significant increases could be found for km split time (p < .001, d = .934) and for HR (p = .010, d = .804). Significant decreases could be found for meanRR (p = .013, d = .798) and DFA-alpha1 (p = .003, d = 1.132). DFA-alpha1 showed an appropriate dynamic range throughout the race consisting of both uncorrelated and anti-correlated values. Lactate was consistent with sustained high intensity exercise when measured at the end of the event. Despite the runners slowing after halfway, DFA-alpha1 continued to fall to values seen in the highest intensity domain during incremental exercise testing in agreement with lactate assessment. Therefore, the discrepancy between the reduced running pace with that of the decline of DFA-alpha1, demonstrate the benefit of using this dimensionless HRV index as a biomarker of internal load during exercise over the course of a marathon race.