Background High-level MYCN amplification (MNA) is associated with poor outcome and unfavorable clinical and biological features in neuroblastoma. Less is known about these associations in patients with low-level MYCN copy number increases. Methods In this retrospective study, we defined patients as having tumors with MYCN wild-type, MYCN gain (2–4 fold increase in MYCN signal compared to reference probe), or MNA (>4 fold increase). We used tests of trend to investigate ordered associations between MYCN copy number category and features of interest. Log-rank tests and Cox models compared event-free (EFS) and overall survival (OS) by subgroup. Results Among 4,672 patients, 3,694 (79.1%) had MYCN wild-type tumors, 133 (2.8%) had MYCN gain, and 845 (18.1%) had MNA. For each clinical/biological feature, the proportion of patients with an unfavorable feature was lowest in the MYCN wild-type category, intermediate in the MYCN gain category, and highest in the MNA category (p<0.0001), except for 11q aberration where the highest rates were in the MYCN gain category. Patients with MYCN gain had inferior EFS and OS compared to wild-type. Among patients with high-risk disease, MYCN gain was associated with the lowest response rate following chemotherapy. Patients with non-stage 4 disease and patients with non-high risk disease with MYCN gain had significantly increased risk for death, a finding confirmed on multivariable testing. Conclusions Increasing MYCN copy number is associated with an increasingly higher rate of unfavorable clinical/biological features, with 11q aberration an exception. Patients with MYCN gain have inferior outcomes, especially in otherwise more favorable groups.