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Variations in autonomic nervous system activity (ANS) and variations in performances have been shown to be correlated at the group level in swimmers. The aim of the study was to investigate the strength of that relationship at the individual level.Seven regional-level swimmers (four male, age 16.6 ± 05 yr, 6.4 ± 0.9 yr of practice) were included in the study. They performed maximal aerobic performance on a 400-m freestyle race before and after a 3-wk intensive training period, and following a 2-wk tapering period. ANS activity was assessed through heart rate variability (HRV) indices measured the night before each race and twice a week along the protocol.All HRV indices were altered, with global and parasympathetic indices decreasing from W1 to W3 in the whole group, while they increased until W5 in five swimmers, and continuously decreased in two. Best performances were respectively realized when global and parasympathetic indices of HRV were highest. Importantly, the relationship between the changes in performances and the changes in HRV indices was strong (ΔPerf = −1.232 to 1.625·ΔHFwavelet, R2 = 0.5); the greater the rebound in ANS activity after W3, the greater the performance improvement, and reciprocally.Performance is correlated with nocturnal ANS activity at an individual level. The decrease in ANS activity during intensive training is correlated with the loss in performance, and the rebound in ANS activity during tapering tracks with the gain in performance. Interestingly, the speed of the rebound during the tapering period was quite different between swimmers. ANS activity measurement may be useful to design and control individual training periods and to optimize the duration of tapering.