Brain Derived Neurotrophic Factor (BDNF) regulates brain synaptic plasticity. BDNF affects serotonin signaling, increases serotonin levels in brain tissue and prevents degeneration of serotonin neurons. These effects have hardly been studied in human brain. We examined the relationship of the functional val66met polymorphism of the BDNF gene to serotonin 1A (5-HT1A) receptor binding in vivo. 50 healthy volunteers (HV) and 50 acutely depressed, unmedicated patients with major depressive disorder (MDD) underwent PET scanning with the 5-HT1A receptor ligand, [11C]WAY-100635 and a metabolite corrected arterial input function. A linear mixed effects model compared 5-HT1A receptor binding potential (BPF, proportional to the number of available receptors) in 13 brain regions of interest between met allele carriers (met/met and val/met) and noncarriers (val/val) using sex and C-1019G genotype of the 5-HT1A receptor promoter functional polymorphism as covariates. There was an interaction between diagnosis and allele (F = 4.23, df = 1, 94, p = 0.042), such that met allele carriers had 17.4% lower BPF than non-met carriers in the HV group (t = 2.6, df = 96, p = 0.010), but not in the MDD group (t = − 0.4, df = 96, p = 0.58). These data are consistent with a model where the met allele of the val66met polymorphism causes less proliferation of serotonin synapses, and consequently fewer 5-HT1A receptors. In MDD, however, the effect of the val66met polymorphism is not detectable, possibly due to a ceiling effect of over-expression of 5-HT1A receptors in mood disorders.