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Background During military deployment, stress regulation is vital to protect against the development of anxiety and trauma-related symptoms. Brain endocannabinoids play an important role in stress regulation and previous research has shown that genetic variations in the FAAH rs324420 polymorphism demonstrate protective effects during stress. In addition, this polymorphism shows interactions with the CRHR1 and CNR1 polymorphisms on anxiety. The present study examines whether genetic variations of the FAAH, CRHR1 and CNR1 polymorphisms interact with the development of anxiety and trauma related symptoms in military veterans. Methods Veterans (N = 949) who went on military deployment and experienced a stressful event were genotyped for FAAH rs324420, CRHR1 rs110402 and CNR1 rs2180619. Anxiety and trauma symptoms were measured pre-deployment and 6 months after deployment. Anxiety was measured with the anxiety subscale of the Symptom Checklist-90 (SCL-90) and trauma with the Self-Rating Inventory for PTSD (SRIP). Results Covariance Pattern Models demonstrated no significant relation of genetic variations in FAAH rs324420 on anxiety and PTSD symptoms from pre-deployment to 6 months after military deployment. Additionally, we investigated interactions between the FAAH s324420, CRHR1 rs110402 and CNR1 rs2180619 polymorphisms. This also demonstrated no significant effects on anxiety and PTSD symptoms pre- to post deployment. However, the covariate of childhood trauma that was included in the models was significant in all these models. Conclusion Genetic variations in FAAH rs324420 and its interactions with CRHR1 rs110402 and CNR1 rs2180619 are not related to the development of anxiety and trauma-related symptoms. The study however, indicates the importance of considering childhood trauma in the investigation of the effects of polymorphisms that are related to the endocannabinoid system on the development of anxiety and PTSD symptoms.