Heart rate variability (HRV) is a known measure of cardiac autonomic function. A cardiovascular autonomic dysfunction (CAD), measured as changes in HRV, is usually presented after an infectious process. The aim of the present study is to assess the association between serum inflammatory markers and CAD. For this purpose, 50 volunteers (13 of them recovering from an infection) were recruited and followed-up for 6 weeks. Their serum inflammatory biomarkers (CRP, IL1, IL4, IL6, IL10, and TNFalpha) were quantified throughout those weeks, along with their HRV resting, in response to the Valsalva maneuver, metronome breathing, standing and sustained handgrip. The correlation of within-subject changes in both HRV and inflammatory biomarkers was assessed to evaluate the concurrent changes. An inverse within-subject correlation was found between CRP and HRV in response to the Valsalva maneuver (rho (95% CI): -0.517 (-0.877 to -0.001); p = 0.032) and HRV standing (rho (95% CI): -0.490 (-0.943 to -0.036); p = 0.034). At the beginning, increased values of CRP are found along with reduced levels of HRV. Then, the CRP was reduced, accompanied by an improvement (increase) in HRV. These results suggest that CRP is a potential marker of CAD. Whether it is the cause, the consequence or a risk indicator non-causally associated is still to be determined.