The prognosis for patients with neuroblastoma is related to the age and stage at time of presentation, as well as to the presence or absence of biological markers such as N-myc amplification and the degree of DNA ploidy. However, previous studies have shown that neuroblastoma in the thoracic site also is a favorable prognostic indicator, in that children with mediastinal neuroblastoma have a better survival rate, regardless of age or stage at time of presentation. This study was designed to evaluate the biological differences between thoracic and nonthoracic neuroblastoma with respect to N-myc amplification, DNA index as a measure of DNA ploidy, serum lactate dehydrogenase levels, and serum ferritin levels. Patients enrolled in the Pediatric Oncology Group study protocols for neuroblastoma were evaluated retrospectively, and log-rank analysis allowed the impact of each biological variable on survival to be determined for each cohort of patients. There were 1,335 neuroblastoma patients in the data base; 227 had thoracic-site neuroblastoma. Through analysis, it was apparent that patients with thoracic neuroblastoma have better survival rates than do their nonthoracic counterparts (P < .0001), and they are less likely to have N-myc amplification (P = .001), more likely to have an LDH level of less than 1,500 (P < .0001), and usually have a DNA index of greater than 1 (P < .003). Both thoracic and nonthoracic patients have low serum ferritin levels (86% of thoracic versus 83% of nonthoracic patients).(ABSTRACT TRUNCATED AT 250 WORDS)