Metamorphosis is a fundamental developmental process and has been intensively studied for various neuron types of Drosophila melanogaster. However, detailed accounts of the fate of identified peptidergic neurons are rare. We have performed a detailed study of the larval morphology and pupal remodelling of identified peptidergic neurons, the CAPA-expressing Va neurons of D. melanogaster. In the larva, Va neurons innervate abdominal median and transverse nerves that are typically associated with perisympathetic organs (PSOs), major neurohaemal release sites in insects. Since median and transverse nerves are lacking in the adult, Va neurites have to undergo substantial remodelling during metamorphosis. We have examined the hitherto uncharacterised gross morphology of the thoracic PSOs and the abdominal median and transverse nerves by scanning electron microscopy and found that the complete reduction of these structures during metamorphosis starts around pupal stage P7 and is completed at P9. Concomitantly, neurite pruning of the Va neurons begins at P6 and is preceded by the high expression of the ecdysone receptor (EcR) subtype B1 in late L3 larvae and the first pupal stages. New neuritic outgrowth mainly occurs from P7-P9 and coincides with the expression of EcR-A, indicating that the remodelling of the Va neurons is under ecdysteroid control. Immunogold-labelling has located the CAPA peptides to large translucent vesicles, which are released from the transverse nerves, as suggested by fusion profiles. Hence, the transverse nerves may serve a neurohaemal function in D. melanogaster.