The circadian rhythm-related aryl hydrocarbon receptor nuclear translocator-like 2 (Arntl2) gene has been identified as a candidate gene for the murine type 1 diabetes locus Idd6.3. Previous studies suggested a role in expansion of CD4 + CD252 T cells, and this then creates an imbalance in the ratio between T-effector and CD4 The murine type 1 diabetes (T1D) locus Idd6 is 1 of ;40 genetic loci identified in the NOD mouse (1). The Idd6 candidate region (2), showing resistance to the spontaneous development of diabetes, overlaps with the candidate region for the resistance of immature T cells to dexamethasone (3-5) and for the control of low rates of proliferation in immature NOD thymocytes (6). Idd6 controls the activity of regulatory CD4 + T cells and invariant natural killer T cells (7,8).Previous research has also focused on the identification of candidate genes and the underlying molecular networks (9-13). The analysis of three NOD.C3H subcongenic strains (6.VIIIa, 6.VIIIb, and 6.VIIIc) derived from the original 6.VIII congenic strain showed the presence of at least three diabetes-related subloci contributing to the overall T1D resistance (Idd6.1, Idd6.2, Idd6.3), but Idd6.3 alone controls the suppressive activity of splenocytes (10).Transcription and sequence analysis revealed aryl hydrocarbon receptor nuclear translocator-like 2 (Arntl2) as candidate gene within Idd6.3. Arntl2 encodes a basic helix-loop-helix/Per-Arnt-Sim transcription factor controlling the circadian rhythm. Arntl2 is upregulated in the spleen and thymus of mice carrying C3H alleles at Idd6.3 compared with mice carrying NOD alleles at the locus. In addition, several polymorphism and different splice forms were identified when comparing the gene and its transcripts in C3H and NOD strains (10). Diabetes incidence is increased by Arntl2 mRNA interference in Idd6 congenic mice concomitant with an increase in CD4 + T cells and a decrease in regulatory CD4 + CD25 + T cells in the peripheral immune system (14). In addition, upregulation of cellular Arntl2 levels correlates with inhibited CD4 + T-cell proliferation and their decreased diabetogenic activity (15).The current study addresses transcriptional changes related to Arntl2 expression in CD4 + T cells. We show that Arntl2 and Idd6.3 control the expression of the interleukin 21 (IL21) gene (Il21) and the number of IL21-producing cells. The promoter of Il21, a gene that codes for an important cytokine involved in the proliferation of T cells, is directly targeted by ARNTL2 in an allele-specific manner. We propose that the circadian rhythm-related Arntl2 gene has specific functions in regulating cytokines involved in T1D.