Objectives. Whereas animal models indicate that brain-derived neurotrophic factor (BDNF) plays a role in anxiety-related behaviour, little is known about BDNF in patients with an anxiety disorder. We tested the hypothesis that serum BDNF levels are low in patients with an anxiety disorder as compared to healthy controls. We further examined the associations of gender and some of the clinical characteristics of anxiety with BDNF levels. Methods. Serum BDNF levels were determined in 393 unmedicated, non-depressed patients with social anxiety disorder, panic disorder, agoraphobia, and generalised anxiety disorder (66.7% females) and in 382 healthy controls (62.0% females). Results. Overall, there were no differences in BDNF levels among patients and controls, regardless of type of anxiety disorder. Analyses stratified by gender revealed that female patients had lower levels of BDNF relative to female controls (P < 0.05, d 0.19), which was stronger in female patients with > 1 anxiety disorder (P < 0.01, d 0.32). BDNF levels were similar among male patients and controls and unrelated to the clinical characteristics of anxiety. Conclusion. Our results mirror preclinical findings indicating that gender plays a role in the association between BDNF and anxiety and suggest that BDNF might play a role in the pathophysiology of anxiety in women. © 2012 Informa Healthcare.