The purpose of this study was to investigate changes in post-exercise heart rate recovery (HRR) and heart rate variability (HRV) during an overload-tapering paradigm in marathon runners and examine their relationship with running performance. 9 male runners followed a training program composed of 3 weeks of overload followed by 3 weeks of tapering (-33 +/- 7%). Before and after overload and during tapering they performed an exhaustive running test (T(lim)). At the end of this test, HRR variables (e.g. HRR during the first 60 s; HRR(60 s)) and vagal-related HRV indices (e.g. RMSSD(5-10 min)) were examined. T(lim) did not change during the overload training phase (603 +/- 105 vs. 614 +/- 132 s; P = 0.992), but increased (727 +/- 185 s; P = 0.035) during the second week of tapering. Compared with overload, RMSSD(5-10 min) (7.6 +/- 3.3 vs. 8.6 +/- 2.9 ms; P = 0.045) was reduced after the 2(nd) week of tapering. During tapering, the improvements in T(lim) were negatively correlated with the change in HRR(60 s) (r = -0.84; P = 0.005) but not RMSSD(5-10 min) (r = -0.21; P = 0.59). A slower HRR during marathon tapering may be indicative of improved performance. In contrast, the monitoring of changes in HRV as measured in the present study (i.e. after exercise on a single day), may have little or no additive value.