Hel-N1 and HuD belong to the elav gene family and encode neuron-specific RNA-binding proteins that are temporally regulated in neural development. Recently, these genes have been detected in small cell lung carcinoma, a neuroendocrine tumor, with HuD down-regulated in poorly differentiated, variant subsets. We, therefore, sought to determine: (a) the extent to which Hel-N1 and HuD are expressed in neuroblastoma (NB); and (b) whether the individual patterns of expression are associated with clinical features of the tumor. We used a sensitive and quantitative RNase protection assay that reliably distinguishes between these homologous genes, and with it we show that Hel-N1 and HuD transcripts were detected in 100% of cultured cells (11 of 11) and 97% of primary tumor samples (35 of 36). Densitometric quantification of transcripts indicated that the levels of HuD and Hel-N1 varied in all samples. In primary NB tissue, samples that expressed the highest Hel-N1 or HuD levels were N-myc unamplified. With HuD, the level in unamplified primary tumors was significantly higher than that of amplified tumors (0.80 +/- 0.12 versus 0.33 +/- 0.12, P < 0.02). HuD expression in prognostically favorable tumor stages was also significantly higher than unfavorable stages (0.98 +/- 0.19 versus 0.47 +/- 0.08, P < 0.03). In summary, the ubiquitous detection of HuD and Hel-N1 in NB indicates that they are molecular neuronal markers of this tumor. Furthermore, high HuD mRNA levels may predict a clinically favorable outcome.