Background: To compare the expression of chemokines in the aqueous humor and chemokine receptors in intraocular lymphocytes from Behçet and non-Behçet uveitis patients. Methods: A total of 95 uveitis patients were included in this study. We studied 39 Behçet and 56 non-Behçet uveitis patients. Flow cytometric analysis was performed using lymphocytes from the aqueous humor and the peripheral blood during the active phase of intraocular inflammation. We compared the expression of CXCR1, CXCR3, and CCR5 in CD4+ and CD8+ T lymphocytes and the concentration of intraocular CXCL8, CXCL10 and CCL5 in Behçet and non-Behçet patients. Results: The CD4+ cell population was higher in the aqueous humor of non-Behçet patients, whereas the CD8+ cell population was higher in the aqueous humor of Behçet patients. The expressions of CXCR1 and CCR5 were not significantly different between the two groups, whereas the intraocular expression of CXCR3 was higher in the CD4+ cells of non-Behçet and in the CD8+ cells of Behçet uveitis patients. Intraocular CXCL8 and CXCL10 levels were higher in Behçet than they were in non-Behçet patients. CCL5 levels were not different between the groups. Conclusions: This suggests that the expression of chemokines and chemokine receptors in intraocular lymphocytes is different in Behçet compared to non-Behçet uveitis patients, which might be related to the differential phenotypes of intraocular lymphocytes among different uveitis etiologies.