BACKGROUND: Individuals suffering from an anxiety disorder are characterized by chronically low heart rate variability (HRV) compared to healthy individuals during resting state conditions. However, when examining HRV and HR in response to a stressor, mixed results have been obtained when comparing anxious and non-anxious groups. METHODS: The primary aim of the present study was to investigate HRV and HR responding in 26 clinically anxious and 14 control individuals before, during and after a stressful working memory task. RESULTS: Results indicate no between-group differences in HRV and HR at baseline. When starting the working memory task, the control group decreased significantly in HRV and the anxious group did not differ substantially in their change pattern from baseline to the start of the stressor. Finally, during the recovery phase of the working memory task, the clinically anxious and control individuals did not differ in their HFV or HR response compared to baseline. CONCLUSIONS: From a clinical perspective, the results suggest that screening for the presence of anxiety disorders may help to identify patients with impaired HRV and HR functioning and to intervene on these important patient characteristics early in the treatment process.