The orexigenic effects of neuropeptide Y (NPY) are mediated through the hypothalamus, while the anxiolytic effects of NPY appear to be mediated through the amygdala. We hypothesized that intra-amygdalar administration of NPY might alter food preference without changing total food intake. Neuropeptide Y was administered into the central nucleus of the amygdala in both satiated and overnight-fasted rats, and intake and preference for a high fat diet (56%)/low carbohydrate (20%) diet or a low fat (10%)/high carbohydrate (66%) diet were measured. Intra-amygdalar NPY administration in satiated rats did not change total caloric intake, but it did produce a dose-dependent decrease in intake of and preference for high fat diet relative to low fat diet over 24 h. In overnight-fasted rats, intra-amygdalar NPY also decreased the intake and preference for a high fat diet relative to low fat diet over 24 h, without altering total caloric intake. Intra-amygdalar NPY administration did not produce conditioned taste aversions to a novel saccharin solution. These results suggest that amygdalar NPY may have a role in macronutrient selection, without altering total caloric intake.