The detrimental sequelae of severe zinc deficiency on the thymus and T-lymphocyte compartment of the mammalian immune system have been established, but underlying mechanisms remain unknown. Hypothesizing that the alterations in T-lymphocyte number and function observed during zinc deficiency may result from changes in gene expression, we sought to compare thymic mRNA expression profiles of zinc-deficient and zinc-normal mice utilizing cDNA arrays. For our murine model described herein, 3 wk of dietary zinc deficiency did not perturb food intake or growth rate in young adult, outbred mice, but significantly depressed multiple parameters of zinc status. Furthermore, fluorescence-activated cell sorting (FACS) analysis demonstrated no changes in thymocyte populations expressing the cell surface markers CD3, CD4 or CD8, establishing that observed changes in mRNA abundances were not attributable to different thymocyte populations. Yet notably, at this moderate level of zinc deficiency, cDNA array analysis identified four potentially zinc-regulated mRNAs whose modulation was confirmed independently, twice, using both semiquantitative and real-time quantitative reverse transcription-polymerase chain reaction. Expression of one of these genes (myeloid cell leukemia sequence-1) was depressed, whereas the others [DNA damage repair and recombination protein 23B, the mouse laminin receptor and the lymphocyte-specific protein tyrosine kinase (LCK)] were elevated in the zinc-deficient mice. Further Western analysis demonstrated that the zinc binding protein LCK was elevated in these zinc-deficient mice. Results demonstrate that 3 wk of dietary zinc insufficiency can alter specific thymic mRNA and protein abundances before alterations occur in thymocyte development as detectable by FACS analysis.