We devised a real-time RT-PCR method for the quantification of preproinsulin 1 and 2, proglucagon, prosomatostatin, and GAD 65 and 67 mRNAs in the thymus, using specific primers and internal probes. Corresponding standard cRNA synthesis and normalization to 18S ribosomal RNA allowed direct quantification. Then, during the first month of life, the expression of each substance of interest was measured in the thymus of NOD mice (a spontaneous model of type 1 diabetes), C57BL/6, BALB/c and lymphocyte-deficient mice (NODscid, NODrag, BALBlcscid and C57BL/6rag). In all mouse thymuses, preproinsulin 1 and GAD 65 were undetectable, preproinsulin 2 and proglucagon showed low expression, whereas that of GAD 67 and somatostatin were high. In 7-day-old mice, GAD 67 and prosomatostatin thymic expressions were lower in NOD than in C57BL/6, and at the same age, the scid mutation but not the rag mutation induced higher expression of all investigated genes compared to control mice. In conclusion, our data allowed the quantification of the expression of pancreatic factors in the mouse thymus. Investigations are underway to quantify, at the cellular level, i.e., in thymic dendritic/macrophage cells, the RNA expression of potential autoantigens, such as preproinsulin 2 and GAD 67.