Decreased heart rate variability (HRV) has both diagnostic and prognostic value in patients with sepsis. However, it is not known whether reduced HRV in sepsis reflects an altered input from the autonomic nervous system or a remodeling of the cardiac pacemaker cells by inflammatory mediators. The present study aimed to investigate the effect of endotoxin on the heart rate dynamics of a denervated isolated heart in rats. Saline or endotoxin was injected into rats and their hearts were isolated and perfused. Atrial electrical activity was recorded and memory length in the time-series was assessed using inverse statistical analysis. Memory was defined as a statistical feature that lasts for a period of time and distinguishes the time-series from a random process. Endotoxaemic hearts exhibited a prolonged memory compared to the controls with respect to observing rare events. This indicates that a sudden decelerating event could potentially affect the cardiac rhythm of an endotoxaemic heart for a longer time than the controls. The prolongation of memory is indirectly linked to a reduced controllability in a complex system; therefore our data may provide evidence for a reduced controllability in cardiac rhythm following endotoxaemia.