We examined the expression of calcium transporter 1 (CaT1) and epithelial calcium channel (ECaC) mRNA in the duodenum and kidney of mice. Intestinal CaT1 mRNA level increased 30-fold at weaning, coincident with the induction of calbindin-D_9k expression. In contrast, renal CaT1 and ECaC mRNA expression was equal until weaning when ECaC mRNA is induced and CaT1 mRNA levels fall 70%. Long- and short-term adaptation to changes in dietary calcium (Ca) level and 1,25 dihydroxyvitamin D₃ [1,25(OH)₂D₃] injection strongly regulated duodenal calbindin D_9k and CaT1 mRNA. Following a single dose of 1,25(OH)₂D₃, induction of CaT1 mRNA occurred rapidly (within 3 h, peak at 6 h of 9.6 ± 0.8-fold) and preceded the induction of intestinal Ca absorption (significantly increased at 6 h, peak at 9 h). Neither renal CaT1 nor ECaC mRNA were strongly regulated by dietary calcium level or 1,25(OH)₂D₃ injection. Our data indicate that CaT1 and ECaC mRNA levels are differentially regulated by 1,25(OH)₂D₃ in kidney and intestine and that there may be a specialized role for CaT1 in kidney in fetal and neonatal development. The rapid induction of intestinal CaT1 mRNA expression by 1,25(OH)₂D₃, and the marked induction at weaning, suggest that CaT1 is critical for 1,25(OH)₂D₃-mediated intestinal Ca absorption.