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Background Neuropeptide Y (NPY) has been implicated in depression, anxiety, and memory. Expression of human NPY and the number of NPY-positive neurons in the rodent amygdala correlate with anxiety and stress-related behavior. Increased NPY expression in the epileptic brain is supposed to represent an adaptive mechanism counteracting epilepsy-related hyperexcitability. We attempted to investigate whether NPY-positive neurons in the human amygdala are involved in these processes. Methods In 34 adult epileptic patients undergoing temporal lobe surgery for seizure control, the density of NPY-positive neurons was assessed in the basal, lateral, and accessory-basal amygdala nuclei. Cell counts were related to self-reported depression, anxiety, quality of life, clinical parameters (onset and duration of epilepsy, seizure frequency), antiepileptic medication, and amygdala and hippocampal magnetic resonance imaging volumetric measures. Results Densities of NPY-positive basolateral amygdala neurons showed significant positive correlations with depression and anxiety scores, and they were negatively correlated with lamotrigine dosage. In contrast, NPY cell counts showed no relation to clinical factors or amygdalar and hippocampal volumes. Conclusions The results point to a role of amygdalar NPY in negative emotion and might reflect state processes at least in patients with temporal lobe epilepsy. Correlations with common clinical parameters of epilepsy were not found. The question of a disease-related reduction of the density of NPY-positive amygdalar neurons in temporal lobe epilepsy requires further investigation.