The neurotrophin brain-derived neurotrophic factor (BDNF) is a key survival factor for neural cells. In particular, in neuroblastoma tumour cells, expression of the BDNF/TrkB autocrine signalling system promotes a more malignant phenotype and resistance to chemotherapy. The human BDNF gene contains two clusters of upstream exons encoding the 5'UTR (exon 1 to exon 3 and exon 4 to exon 9a), these are alternatively spliced to a common exon 9, which contains the coding region and the 3'UTR. At least 34 different BDNF mRNA transcripts can be generated, although their physiological role is still unknown. The purpose of this study is to determine which BDNF transcript is involved in cell survival of the human neuroblastoma cell lines SH-SY-5Y (single-copy MYCN) and SK-N-BE (amplified MYCN). Expression of human BDNF mRNAs encoding all possible isoforms was characterised in the two neuroblastoma cell lines. We then investigated whether selective silencing of the different BDNF mRNAs using specific siRNAs could reduce cell survival in response to serum deprivation or the anticancer drugs cisplatin, doxorubicin and etoposide. We found that three isoforms located in the second exon cluster are essential for neuroblastoma cell survival under cytotoxic stress. Notably, promoters of the second exon cluster, but not the first, are controlled by Ca(2+)-sensitive elements.