Vocal learning and neuronal replacement have been studied extensively in songbirds, but until recently, few molecular and genomic tools for songbird research existed. Here we describe new molecular/genomic resources developed in our laboratory. We made cDNA libraries from zebra finch (Taeniopygia guttata) brains at different developmental stages. A total of 11,000 cDNA clones from these libraries, representing 5,866 unique gene transcripts, were randomly picked and sequenced from the 3 ends. A webbased database was established for clone tracking, sequence analysis, and functional annotations. Our cDNA libraries were not normalized. Sequencing ESTs without normalization produced many developmental stage-specific sequences, yielding insights into patterns of gene expression at different stages of brain development. In particular, the cDNA library made from brains at posthatching day 30 -50, corresponding to the period of rapid song system development and song learning, has the most diverse and richest set of genes expressed. We also identified five microRNAs whose sequences are highly conserved between zebra finch and other species. We printed cDNA microarrays and profiled gene expression in the high vocal center of both adult male zebra finches and canaries (Serinus canaria). Genes differentially expressed in the high vocal center were identified from the microarray hybridization results. Selected genes were validated by in situ hybridization. Networks among the regulated genes were also identified. These resources provide songbird biologists with tools for genome annotation, comparative genomics, and microarray gene expression analysis.cDNA microarray ͉ developmental gene expression ͉ EST sequencing ͉ microRNA ͉ zebra finch T he genomes of many species, including human, mouse, chicken, Drosophila, Caenorhabditis elegans, and zebrafish, have been sequenced, with the result that genomic, computational, and microarray tools have greatly accelerated discoveries in many fields of biology. However, the availability of such resources has lagged in songbirds, even as two species, the zebra finch (Taeniopygia guttata) and the canary (Serinus canaria), have received much attention from scientists studying the biology of vocal learning and neuronal replacement in the adult brain. Songbirds have been proven to be exceedingly favorable material for studying the basic biology of these two phenomena. Here we describe our effort to develop molecular resources that can be used in such work, including the large-scale sequencing of ESTs and the printing of cDNA microarrays of genes expressed in zebra finch brains. The high vocal center (HVC) controls song learning in juveniles and song production in adult birds and is also a place where neuronal replacement occurs in adulthood (1). We used microarrays to profile genes differentially expressed in the HVC of adult male zebra finches and canaries, compared with universal total brain RNA references, and validated the microarray results by in situ hybridization.