Cardiac arrhythmias are associated with an increase in sympathetic activity (reflected in increased heart rate) and a simultaneous decrease in rhythmical fluctuations of sympathetic activity [reflected in decreased heart rate variability (HRV)]. As hypoxia is a well known trigger for cardiac arrhythmias, and carbohydrate loading a known sympatho-excitatory stimulus, the present study investigated if carbohydrate loading affects the cardiac response to acute hypoxic challenge. Fourteen subjects ingested a sucrose solution or an equal volume of water and spectral analysis of HRV was used to determine HRV components in normoxia and acute, normobaric hypoxia. Compared to the control condition, ingestion of carbohydrates increased heart rate, spectral power of nLF (P < 0.02) and LF/HF ratio (P < 0.003), and decreased spectral power of nHF (P < 0.03) during hypoxia. Carbohydrate ingestion thus intensified cardiac autonomic modulation during acute hypoxia and may therefore act as a beneficial protective mechanism against the disturbances of cardiac rhythm in hypoxic conditions.