High performing dairy cows experience distinct metabolic stress during periods of negative energy balance. Subclinical disorders of the cow’s energy metabolism facilitate failure of adaptational responses resulting in health problems and reduced performance. The autonomic nervous system (ANS) with its sympathetic and parasympathetic branches plays a predominant role in adaption to inadequate energy and/or fuel availability and mediation of the stress response. Therefore, we hypothesize that indices of heart rate variability (HRV) that reflect ANS activity and sympatho-vagal balance could be early markers of metabolic stress, and possibly useful to predict cows with compromised regulatory capacity. In this study we analysed the autonomic regulation and stress level of 10 pregnant dried-off German Holstein cows before, during and after a 10-h fasting period by using a wide range of HRV parameters. In addition heat production (HP), energy balance, feed intake, rumen fermentative activity, physical activity, non-esterified fatty acids, β-hydroxybutyric acid, cortisol and total ghrelin plasma concentrations, and body temperature (BT) were measured. In all cows fasting induced immediate regulatory adjustments including increased lipolysis (84%) and total ghrelin levels (179%), reduction of HP (−16%), standing time (−38%) and heart rate (−15%). However, by analysing frequency domain parameters of HRV (high-frequency (HF) and low-frequency (LF) components, ratio LF/HF) cows could be retrospectively assigned to groups reacting to food removal with increased or decreased activity of the parasympathetic branch of the ANS. Regression analysis reveals that under control conditions (feeding ad libitum) group differences were best predicted by the nonlinear domain HRV component Maxline (LMAX, R2=0.76, threshold; TS=258). Compared with cows having LMAX values above TS (>LMAX: 348±17), those with LMAX values below TS (<LMAX: 109±26) had higher basal blood cortisol levels, lower concentrations of insulin, and respond to fasting with a shift of their sympatho-vagal balance towards a much stronger dominance of the sympathetic branch of the ANS and development of stress-induced hyperthermia. The data indicate a higher stress level, reduced well-being and restricted regulatory capacity in <LMAX cows. This assumption is in accord with the lower dry matter intake and energy corrected milk yield (16.0±0.7 and 42±2 kg/day) in lactating <LMAX compared with >LMAX cows (18.5±0.4 and 47.3 kg/day). From the present study, it seems conceivable that LMAX can be used as a predictive marker to discover alterations in central autonomic regulation that might precede metabolic disturbances.