The neonatal visual cortex is a highly plastic structure and its development is guided by visual experience during early postnatal life. Rats do not open their eyes until the end of the second postnatal week. We hypothesized that the expression of genes in the visual cortex would differ before and after eye opening. As a first step in uncovering these differences, we compared gene expressions in the visual cortex of postnatal days (PND) 1 and 21 rats. Suppression subtractive hybridization was performed using PND1 samples as the tester and PND21 as the driver. More than 30 genes were expressed at a higher level in PND1 than PND21 samples, but 5 fragments showed higher copies than others. PCR product of the five fragments was gel-purified and cloned into pCRII vectors. They showed significant homology to cDNA of genes: (A). clone MGC: 19375; (B). Type II iodothyronine 5'-deiodinase (D2); (C). reduced expression 3 gene; (D). lactosylceramide synthase; and (E). septin 4, respectively. Functions of A, C and E are unknown. By means of RACE PCR, three full-length cDNAs not reported previously in the rat were obtained for A, C and E, and we named them "expression genes 1, 2 and 3, respectively, in the rat visual cortex (EG1RVC, EG2RVC and EG3RVC)". EG1RVC was further characterized by Northern blots, in situ hybridization and in vitro transfection. These approaches confirmed that EG1RVC was expressed at a significantly higher level in PND1 than in PND21 visual cortical samples, and that transfected PC12 cells and primary neuronal cultures showed expression mainly in neuronal cell bodies. Our data indicate that genes expressed more abundantly on PND1 are associated with various metabolic pathways and enzymatic changes, and may play an important role in visual cortical development, growth and/or plasticity.