C2H2-type zinc finger genes comprise one of the largest gene families in the human genome. These proteins are involved in genetic regulation and development and are quite conserved throughout evolution. The finger domains commonly contain the small linker peptide TGEKP between some finger units. Here, we report the isolation of 133 human zinc finger cDNAs, of which 118 are novel. These clones were isolated from human brain cDNA libraries using oligonucleotide hybridization followed by expressed sequence tag (EST) analysis, sequencing from the conserved linker region using degenerate oligonucleotide primers. This directed partial sequencing approach to cDNA isolation and characterization, signature sequencing, combines the speed of EST automatic sequencing with the focus of specific cDNA family analysis. Signature sequencing minimizes the generation of less informative random EST sequences and provides a unique relative position for sequence comparison. We also show that there is an even distribution of these RNAs from this brain cDNA library, and that these cDNAs contain N-terminal domains found in other zinc finger genes. This rapid focused sequencing approach should be applicable to any family of cDNAs containing short conserved signature peptide sequences.