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Background The serotonergic and the endocannabinoid system are involved in the etiology of depression. Depressive patients exhibit low serotonergic activity and decreased level of the endocannabinoids anandamide (AEA) and 2-arachidonylglycerol (2AG). Since the cannabinoid (CB) 1 receptor is activated by endogenous ligands such as AEA and 2AG, whose concentration are controlled by the fatty acid amide hydrolase (FAAH) and monoacylglycerol lipase, respectively, we investigated the effects on serotonergic utilization. In this study, we investigated the impact of the rs1049353 single-nucleotide polymorphism (SNP) of the cannabinoid receptor 1 ( CNR1 ) gene, which codes the endocannabinoid CB1 receptor, and the rs324420 SNP of the FAAH gene on the serotonergic and endocannabinoid system in 59 healthy volunteers. Methods Serotonergic activity was measured by loudness dependence of auditory-evoked potentials (LDAEP). Plasma concentrations of AEA, 2AG and its inactive isomer 1AG were determined by mass spectrometry. Genotyping of two SNPs ( rs1049353, rs344420 ) was conducted by polymerase chain reaction (PCR) and differential enzymatic analysis with the PCR restriction fragment length polymorphism method. Results Genotype distributions by serotonergic activity or endocannabinoid concentration showed no differences. However, after detailed consideration of the CNR1 -A-allele-carriers, a reduced AEA (A-allele-carrier M  =  0.66 , SD =  0.24 ; GG genotype M  =  0.72 , SD =  0.24 ) and 2AG (A-allele-carriers M  =  0.70 , SD =  0.33 ; GG genotype M = 1.03, SD =  0.83 ) plasma concentration and an association between the serotonergic activity and the concentrations of AEA and 2AG has been observed. Conclusions Our results suggest that carriers of the CNR1-A allele may be more susceptible to developing depression.