PURPOSE: To determine whether HR variability (HRV), an indirect measure of autonomic control, is associated with upper respiratory tract and pulmonary infections, muscular affections, and all-type pathologies in elite swimmers. METHODS: For this study, 7 elite international and 11 national swimmers were observed weekly for 2 yr. The indexes of cardiac autonomic regulation in supine and orthostatic position were assessed as explanatory variables by time domain (SD1, SD2) and spectral analyses (high frequency [HF] = 0.15-0.40 Hz, low frequency [LF] = 0.04-0.15 Hz, and HF/LF ratio) of HRV. Logistic mixed models described the relationship between the explanatory variables and the risk of upper respiratory tract and pulmonary infections, muscular affections, and all-type pathologies. RESULTS: The risk of all-type pathologies was higher for national swimmers and in winter (P < 0.01). An increase in the parasympathetic indexes (HF, SD1) in the supine position assessed 1 wk earlier was linked to a higher risk of upper respiratory tract and pulmonary infections (P < 0.05) and to a higher risk of muscular affections (increase in HF, P < 0.05). Multivariate analyses showed (1) a higher all-type pathologies risk in winter and for an increase in the total power of HRV associated with a decline SD1 in supine position, (2) a higher all-type pathologies risk in winter associated with a decline in HF assessed 1 wk earlier in orthostatic position, and (3) a higher risk of muscular affections in winter associated with a decrease SD1 and an increase LF in orthostatic position. CONCLUSIONS: Swimmers' health maintenance requires particular attention when autonomic balance shows a sudden increase in parasympathetic indices in the supine position assessed 1 wk earlier evolving toward sympathetic predominance in supine and orthostatic positions.