Background When depressive symptoms in bipolar and unipolar patients were compared, a number of studies reported that atypical vegetative features such as hypersomnia and hyperphagia were more common in bipolar patients. Moreover, neuropeptides such as orexin-A (ORX-A), ghrelin (GRL), and neuropeptide Y (NPY) are involved in the regulation of these vegetative functions. Materials and methods A total of 45 unipolar and 24 bipolar depressive patients, and 36 euthymic healthy controls were included in the study. The groups were compared in terms of peripheral blood samples of ORX-A, GRL, and NPY levels, as well as HAM-D, Epworth Sleepiness Scale, Three-Factor Eating Questionnaire-Revised, and Suicide Probability Scale scores. Results Both unipolar and bipolar patients had lower ORX-A, GRL, and NPY levels compared to the controls, whereas NPY levels of bipolar patients were lower than unipolar patients. There was a negative correlation between NPY levels and emotional eating in the bipolar group. Conclusion While lower ORX-A, GRL, and NPY levels are associated with depressive episodes regardless of the diagnosis; NPY levels also differ in bipolar and unipolar depression patients.