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As a first approach to study the molecular mechanisms that underlie the effects of thyroid hormones on the developing brain, we used a cDNA microarray technology to identify early thyroid hormone-regulated genes in brain neuronal cultures treated with tri-iodothyronine (T3) for 3 h. We identified three genes that were up-regulated by T3, basic transcription element-binding protein, nuclear pore glycoprotein and bone morphogenetic protein-4 and one that was down-regulated, the neuronal apoptosis-inducing gene. We confirmed that these genes were also regulated by the thyroid state in the developing brain. Our findings enrich our knowledge of signaling pathways regulated by thyroid hormones and open new avenues for studying the molecular mechanisms of thyroid hormones in the developing brain.