BACKGROUND: Heart rate variability (HRV) is defined as variations in R-R interval with time. Dysautonomia is common in patients with psychiatric disorders such as depression and anxiety. Using HRV analysis, recent studies showed that in anxiety disorders, the vagal cardiac function decreases, and sympathetic function increases. This study aimed at investigating citalopram effects on HRV. METHODS: This before and after study was conducted in 25 generalized anxiety disorder (GAD) patients. GAD was diagnosed based on clinical interview according to diagnostic and statistical manual of mental disorders IV-Text revised (DSM-IV-TR) criteria using Structured Clinical Interview for DSM Disorders-I questionnaire. A cardiologist studied 24 h ambulatory monitoring of the electrocardiogram (Holter) on all patients before the treatment. A volume of 20 mg of citalopram was administered to the subjects on a daily basis. Then, they were studied by Holter monitoring again after 1-month of administration of citalopram. RESULTS: The average age of participants was 35.32 ± 8.7. The average Holter monitoring time was 23.29 ± 1.14 h before treatment and 23.81 ± 0.68 after it. The 3 h low frequency/high frequency ratio was significantly different between 3 h segments of time before treatment (P < 0.001). This difference was even higher after treatment (P = 0.001). Data showed an increase in parasympathetic tone during sleep both before and after treatment. CONCLUSION: These patients showed some impairments of HRV indices that did not improve by citalopram in future, the clinical importance of such disturbances should be evaluated in details with prolonged follow-up and greater sample size.