It is well-known that the small intestine of rodents rapidly undergoes differentiation and maturation during the transient suckling-weaning period from postnatal days 13 to 27. In the present study, we examined the gene expression changes in the jejunum of rats during the transient suckling-weaning period by microarray analysis. In the microarray data, we found that the expressions of many genes related to digestion/absorption/excretion of nutrients/ions, such as members of the solute carrier (Slc) family and ATP-binding cassette (Abc) subfamily, were rapidly induced during this period. Furthermore, some transcriptional factors/cofactors (Thrsp, Ppargc1a, Klf15 and Vdr), which are presumably important for the induction of intestinal gene expression after weaning, were rapidly induced during this period. In contrast, genes related to transport of nutrients, such as folate, zinc, fat and phosphate, which are important for early development, were highly expressed in the suckling period and then gradually decreased during weaning. These results indicate that the jejunum matures during the suckling-weaning period accompanied by changes in the expression of many genes related to digestion/absorption/excretion and some genes for transcriptional factors/cofactors.