Metallothionein (MT) can modulate transcriptional activity in vitro. We examined whether the absence of MT affects gene expression in vivo. We compared the hepatic RNA profiles of wild-type and MT-null neonatal mice using improved differential display. The hepatic MT level was maximal during neonatal development. We identified five cDNA fragments that were expressed in MT-null mice at different levels from those in wild-type mice. Two were fragments of MT-I and mutant MT-I cDNA. The sequences of the other cDNA fragments were identical to those of contrapsin, transketolase, and vanin-3. The latter two were upregulated, whereas contrapsin was down-regulated in neonatal MT-null mice. These mRNA levels were remarkably different between the two strains of neonatal mice. Further characterization of the regulated mRNA identified here will determine whether or not they are primary or secondary effects of an MT deficiency.