We report a case of pneumococcal arthritis occurring in a 15-year-old boy following allogeneic BMT. The post-transplant course was complicated by GVHD requiring prolonged immunosuppressive therapy. He experienced recurrent infections, including pneumococcal pneumonia. Thirty-five months after BMT and 12 months after the pneumococcal pneumonia, pneumococcal arthritis of the left knee occurred. This is the first reported case of arthritis caused by Streptococcus pneumoniae after allogeneic BMT. Penicillin prophylaxis may be used to prevent recurrence of pneumococcal infections in patients with chronic GVHD.