Septic arthritis and osteomyelitis in children is seldom accompanied by calf vein thrombosis and rarely by atrial thrombosis. We report the case of an 11-year, 5-month-old boy with septic arthritis and osteomyelitis of the sacroiliac region who developed deep venous thrombosis, in addition to life-threatening right atrial thrombosis. After an intensive hematologic investigation, a hereditary protein C deficiency was revealed. The association of venous thrombosis with septic arthritis or osteomyelitis should raise the possibility of the presence of protein C deficiency.