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Aim In this study we sought to assess whether in elite athletes the physiological increase in cardiac mass attending severe long-term training leading to athlete's heart is accompanied by an improvement of autonomic performance, as assessed by post exercise vagal indices and a novel unitary Autonomic Nervous System Index for sports (ANSIs).Methods The study involved 500 elite athletes (23.9 ± 6.4 years) participating in a screening organised by the National Italian Olympic Committee. All subjects underwent a complete medical examination, rest and stand autonomic assessment (heart rate variability) as well as bicycle exercise. ANSIs was also derived as radar plot from rest, stand and heart rate recovery individual proxies of autonomic nervous system regulation. All subjects were grouped into those with left ventricular hypertrophy present (LVH(+)), or not (LVH(–)), according to recognised thresholds.Results We observed that LVH(+) athletes (24.8%) showed a marked increase of post-exercise vagal indices (p< 0.001) and of ANSIs (p< 0.001), while no difference was observed for heart-rate variability indices. These changes were contingent upon sport intensity categories.Conclusions Elite athletes with physiological cardiac hypertrophy (LVH(+)) present a selective profile of indices of autonomic nervous system performance, characterised by increases of markers of vagal recovery and of the novel unitary autonomic index for sports while RR variance and spectral indices seem to be unmodified. Athlete's heart may be characterised by a specific combination of anatomical and neurocardiac remodeling. This approach might furnish potential warning signs differentiating normal training induced physiology from pathological adaptation.