Anti-tumor necrosis factor (TNF) treatment has been a breakthrough in the management of juvenile idiopathic arthritis (JIA). However, they are associated with a significant risk of tuberculosis. We evaluated JIA patients who received etanercept treatment from an eastern Mediterranean country with moderate tuberculosis frequency. JIA patients under anti-TNF treatment, etanercept, were enrolled to the study. Chest X-rays, Tuberculin Skin Test (TST), clinical histories, family screening, and physical examinations were reviewed retrospectively. If TST was above 10 mm in a patient with one Bacillus Calmette-Guerin, cultures and, if needed, thorax computerized tomography were obtained. These patients received 1-2 months of isoniazid (INH) treatment which was followed by an INH prophylaxis for a period of 9 months while etanercept treatment was started. All were re-evaluated within 3 months intervals. A total of 36 patients under etanercept treatment were enrolled to the study. Mean age of the patients was 14.00 years (range 4-22 years). Median duration of disease was 36.00 months (range 4-216 months). Median duration of etanercept therapy was 11.5 months (3-48 months) at final evaluation. Seven patients had an initial TST score above 10 mm. All received INH treatment as outlined above. They had normal examinations and X-rays during follow-up. With proper initial evaluation, anti-TNF treatment is safe even in countries where tuberculosis is moderately frequent. An initial 1-2 months of INH treatment followed by chemoprophylaxis for 9 months is suggested for children with a TST of > 10 mm.