Large-scale hemizygous loss of chromosome 3p is a common event in neuroblastoma, occurring preferentially in tumors that exhibit loss of chromosome 11q and lack MYCN amplification. Although numerous tumor suppressor genes (TSG) have been mapped to the 3p region, the gene or genes contributing to neuroblastoma pathogenesis have remained elusive. High-resolution oligonucleotide array CGH mapping of chromosome 3p breakpoints relative to the positions of known TSGs indicates that more than one gene may contribute to neuroblastoma pathogenesis. We evaluated the methylation status of semaphorin 3B (SEMA3B), one of the chromosome 3p TSGs, in neuroblastoma tumors with (n = 12) and without (n = 32) 3p deletions. A significantly higher percentage of methylated CpG sites in the SEMA3B promoter was detected in tumors exhibiting 3p loss (95%), relative to tumors without loss (52%), suggestive of a two-hit mechanism of allele inactivation. The involvement of methylation in the control of SEMA3B expression was confirmed by treatment of neuroblastoma cell lines with the demethylating agent 5-aza-2-deoxycytidine. Transcriptional regulation of this locus is complex, however; low levels of SEMA3B expression were also seen in tumors with unmethylated SEMA3B promoters (n = 4). SEMA3B is known to play an important role in the development of normal sympathetic neurons, and interestingly, we found higher levels of SEMA3B expression in differentiated tumors with favorable histopathology (n = 19) than in tumors with unfavorable histology (n = 22). Furthermore, SEMA3B was upregulated in the SK-N-BE neuroblastoma cell line following induction of differentiation with retinoic acid. The association of SEMA3B expression with neuroblastoma differentiation suggests that this TSG may play a role in neuroblastoma pathobiology.