Neuropeptide Y (NPY) is a sympathetic neurotransmitter highly expressed in neuroblastoma (NB). NPY, acting via its Y5 receptor (Y5R), stimulates NB cell survival and chemoresistance, while NPY/NPY5R expression is elevated in NB cell lines and tissues derived from post-chemotherapy patients. However, the mechanisms underlying NPY/Y5R axis activation in these tumors remain unclear. The aim of this work was to investigate the copy number status of the NPY and NPY5R in NB, as well as other copy number alterations (CNAs) that may be present in chemoresistant tumors. 85 tissue samples, including specimens from the primary tumors, distant metastases and local relapses, before and after therapy, were collected from the Hospital Pequeno Principe, Parana, Brazil. CNAs for NPY, NPY5R and MYCN were investigated using TaqMan copy number assay. Additionally, wide genome array-CGH analysis was performed in 12 paired high-risk neuroblastoma cases at diagnosis and at relapse. Copy number for the NPY gene was significantly increased in the post-chemotherapy cases, when compared to the untreated cases (P=0.03), independently of the MYCN status. Among post-treatment samples, there was a significant increase in NPY gene copy number in distant metastases as compared to local relapse (P=0.03) in patients with non MYCN-amplified tumors. Similarly, significant increase in NYP5R gene copy number in post-chemotherapy cases, as compared to untreated cases, was observed only in subpopulation of patients without MYCN amplification. Array-CGH analyses demonstrated no increase in the total number of CNAs in NB relapses. Losses at chromosome 10 (10p15.3 and 10q11.2), which were present in 33% of the pre-treatment and absent in all post-treatment cases, were the only significantly different abnormality between these two groups of patients. Altogether, our data demonstrates CNA of the NPY and NPY5R genes in NB and implicate increase in their copy number as one of the potential mechanisms leading to activation of NPY/Y5R axis in chemoresistant tumors.