An improved method for constructing and screening subtractive cDNA libraries has been used to identify 46 mRNA transcripts that are expressed selectively in neonatal rat dorsal root ganglia (DRG) as judged by Northern blots and in situ hybridization. Sequence analysis demonstrates that both known (e.g. peripherin, calcitonin gene-related peptide, myelin P0) and novel identifiable transcripts (e.g. C-protein-like, synuclein-like, villin-like) are present in the library. Half of the transcripts (23) are undetectable in liver, kidney, heart, spleen, cerebellum, and cerebral cortex. Of the DRG-specific transcripts, 12 contain putative open reading frames that show no identity with known proteins. The construction of such a subtractive library thus provides us with both known and novel markers, and identifies new predicted DRG-specific proteins. In addition, the DRG-specific clones provide probes to define the regulatory elements that specify peripheral nervous-system-specific gene expression.