Chromosomal abnormalities are common characteristics of neuroblastoma, and have been associated with treatment, relapse and survival risk factors. The processes governing the incidence or advancement of chromosomal copy number abnormalities remain unclear, despite progress in understanding their prognostic implications. The present study aimed to provide a comprehensive understanding of genetic alterations, clinical implications, and the association between copy number aberrations (CNAs) and clinical parameters. Single nucleotide polymorphism (SNP) array analysis was performed on a set of 45 neuroblastoma samples to examine chromosomal CNAs and SNPs. Logistic regression analysis was performed to identify SNPs associated with adverse drug reactions (ADRs). In the present study, numerous CNAs were observed in 92% of neuroblastoma tumors, while CNAs were found in 15% of ganglioneuroblastoma tumors. The segmental alterations were mainly observed in stage 3 or 4 neuroblastoma cases that had tumor sizes >10 cm. The present study concentrated on analyzing entire chromosome modifications and revealed that, in contrast to gain, loss of heterozygosity (LOH) mostly occurred during stages 3 and 4 of neuroblastoma. Only stage 3 and 4 neuroblastomas with tumor sizes >10 cm were found to exhibit loss of the Y chromosome, which was associated with similar clinical characteristics as segmental alterations. LOH of the whole chromosome might be a subgroup of whole chromosome alterations, and could be a novel prognosis and treatment marker. Using a regression model, 13 SNPs were identified to be strongly associated with ADRs following chemotherapy for neuroblastoma. Although validation studies in independent cohorts are required, the present findings support the use of CNAs and SNPs for predicting neuroblastoma treatment outcomes.