Metallothioneins (MTs) perform important regulatory and cytoprotective functions in tissues including the brain. While it is known that energy restriction (ER) and dietary -3 polyunsaturated fatty acid (PUFA) deficiency impact postnatal brain growth and development, little data exist regarding the impact of undernutrition upon MT expression in growing animals. We tested the hypothesis that ER with and without dietary -3 PUFA deficiency reduces MT expression in juvenile rats. ER rats were individually pair-fed at 75% of the ad libitum (AL) intake of control rats provided diets consisting of either soybean oil (SO) that is α-linolenic acid (ALA; 18:3 -3) sufficient or corn oil (CO; ALA-deficient). Fatty acids (FA) and metal concentrations of liver and brain regions were analyzed. Tissue expression of MTs ( ) and modulators of MT expression including glucocorticoid receptors ( and ) and several mediators of thyroid hormone regulation ( , , , , and ) were measured. Plasma corticosterone and triiodothyronine levels were also evaluated. ER, but not metal deficiency, reduced expression in the cerebellum (50%) and cerebral cortex (23%). In liver, a reduction in dietary -3 PUFA reduced , , , , and . ER elevated , , and and reduced in the liver. Given MT's role in cellular protection, further studies are needed to evaluate whether ER or -3 PUFA deficiency may leave the juvenile brain and/or liver more susceptible to endogenous or environmental stressors.