Objective Macrophage activation syndrome (MAS) is a severe, potentially life-threatening clinical condition. The clinical features including precipitating events, clinical presentations, treatment strategies, outcome in systemic onset juvenile idiopathic arthritis (So-JIA) children with MAS were reviewed. Perforin A91V gene analysis was also performed. Methods Retrospective review of fourteen MAS cases with So-JIA from 2003 to 2008 from a collected database. Gene-specific polymerase chain reaction ( PCR) primers were used to analyze the perforin A91V gene polymorphism. Results Fourteen patients with age from 4 months to 12 years were considered to have evidence of MAS. Nine of them were boys. The primary diagnosis was systemic onset juvenile idiopathic arthritis. No medication was identified as trigger. Eleven of them had infections prior to MAS. Among them specific infectious agents were identified in four patients. High fever, new onset of hepatosplenomegaly, lymphadenopathy, liver function abnormality, abnormal lipid metabolism and hemophagocytosis were common clinical features. Two cases presented with acute respiratory distress syndrome (ARDS). Multiple organ failure (MOF) occurred in three cases. Three patients died. The variant form (NCBI: SNP rs35947132) of perforin A91V gene was detected in seven systemic onset juvenile idiopathic arthritis compolicated with MAS cases. However no mutation was detected. Clucocorticoid, intravenous immunoglobulin, immunoimpressive therapy were effective treatment of this condition. Plasmapheresis (HP) was successfully used in one case with severe MAS. Conclusions MAS is a rare and potentially fatal complication of childhood rheumatoid diseases such as systemic onset juvenile idiopathic arthritis. In this series, majority of them were male and most of them were preceded by infection. Bone marrow studies support the diagnosis. MOF may be a poor prognostic sign of So-JIA. Aggressive and early therapy is essential. There is no relationship between the variant form (NCBI: SNP rs35947132) of perforin A91V gene and So-JIA with MAS in this small sample's study. More research need to be done by increasing sample's numbers.