Although leukocytapheresis (LCAP) has been reported to be effective for the treatment of various autoimmune disorders, little information has been published yet on the efficacy and safety of LCAP for the treatment of systemic-onset juvenile idiopathic arthritis (SOJIA). A pilot trial of LCAP was therefore conducted on two children with refractory SOJIA using a granulocyte apheresis filter packed with cellulose acetate beads in an attempt to control the disease flares. Following three to eight sessions of LCAP, the joint symptoms gradually resolved without any increase in the dose of corticosteroids. The procedure was associated with a decrease in the serum interleukin-6. No severe adverse effects were observed except for mild nausea. However, efficacy of LCAP sustained in a short time since both patients subsequently developed flares after 3 months of the treatment.