The chemokine CCL21 plays an important role in homing of naive T cells and dendritic cell (DC) to lymph nodes but factors regulating its expression are not fully understood. Migratory DCs are crucial in establishing tolerance towards foreign yet harmless antigens. We discovered that CCL21 is almost completely absent in ileitis-prone SAMP1/YitFc (SAMP) mice, and DC migration is severely impaired. To study molecular basis for reduced production of CCL21 we measured gene expression in lymph node stromal cells and conducted genetic experiments to isolate region responsible for the defect. We used SAMP mice, which develop spontaneous chronic ileitis similar to Crohn's disease. We measured CCL21 expression by quantitative polymerase chain reaction and immunofluorescence, and spontaneous or induced DC migration by flow cytometry. The impact of DC trafficking on ileitis was assessed by feeding mice with the Toll-like receptor 7 ligand R848. To find genetic region conveying defective production of Ccl21 we backcrossed the offspring of SAMP mice and C57/Bl6 mice to the SAMP background and performed high-density SNP mapping. We studied gene expression by nanoString and chromatin structure by ATACseq. SAMP mice express almost no CCL21. Loss of CCL21 expression was linked to a recessive locus on chromosome 4, located adjacent to CCL21 genes. Stromal cells from MLN of SAMP mice had upregulated genes related to antigen presentation and a signature of interferon response. SAMP mice had severe defect of CD11b+CD103+ DC migration from the ileal lamina propria to the mesenteric lymph nodes (MLN), similar to the defect seen in mice lacking CCR7, the receptor for CCL21. Treatment with R848 enhanced DC migration, increased Tregs in MLN and dramatically improved disease scores. We identify the absence of CCL21 as the major pathogenic defect contributing to ileitis in SAMP mice. Identified genetic defect offers new insights into the regulation of CCL21 expression. Our data suggest that therapies aimed at improved DC trafficking might be useful in patients with Crohn's disease.