BACKGROUND: Developmental coordination disorder (DCD) is a diagnosis for children who present with movement difficulties, but are of normal intelligence without neurological deficits. Previous studies have demonstrated that children with DCD exhibit perceptual deficits and lower cognition performance. To date, their autonomic nervous system (ANS) responses during tasks requiring cognitive and perceptual effort have not been compared to typically developing children (TDC). OBJECTIVE: The present study investigated heart rate variability (HRV) as a marker for ANS response differences between DCD and TDC, and the impact of different levels of task difficulty. METHODS: Participants were 60 individuals (9-10 years); 30 children at risk for DCD, and 30 TDC. Each participant performed two tasks each of which demanded enhanced cognitive effort: a visual signal detection task and a digit memory task-each task had two levels of difficulty, low (LD) and high (HD). Heart rate responses were continuously recorded during performance of each task. Frequency domain analysis and heart rate sample entropy (SampEn) were computed to determine ANS responses in each of the tasks. RESULTS: HRV differences were detected between the two levels of task difficulty, LD and HD, for the visual signal detection task, but not for the digit memory task. HRV differences between LD and HD conditions were greater for TDC children than DCD when engaged in visual signal detection task, compare to the memory task. INTERPRETATION: The results suggest that children at risk for DCD may show decreased HRV as a marker for altered ANS responses and potential deficits in the linkage between their perceptions and actions.